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Advances in Intelligent Systems and Computing 616
Mohd Saberi Mohamad
Miguel Rocha
Juan F. De Paz
Tiago Pinto Editors
11th International
Conference on Practical
Applications of
Computational Biology
& Bioinformatics
Advances in Intelligent Systems and Computing
Volume 616
Series editor
Janusz Kacprzyk, Polish Academy of Sciences, Warsaw, Poland
e-mail: kacprzyk@ibspan.waw.pl
About this Series
The series “Advances in Intelligent Systems and Computing” contains publications on theory,
applications, and design methods of Intelligent Systems and Intelligent Computing. Virtually
all disciplines such as engineering, natural sciences, computer and information science, ICT,
economics, business, e-commerce, environment, healthcare, life science are covered. The list
of topics spans all the areas of modern intelligent systems and computing.
The publications within “Advances in Intelligent Systems and Computing” are primarily
textbooks and proceedings of important conferences, symposia and congresses. They cover
significant recent developments in the field, both of a foundational and applicable character.
An important characteristic feature of the series is the short publication time and world-wide
distribution. This permits a rapid and broad dissemination of research results.
Advisory Board
Chairman
Nikhil R. Pal, Indian Statistical Institute, Kolkata, India
e-mail: nikhil@isical.ac.in
Members
Rafael Bello Perez, Universidad Central “Marta Abreu” de Las Villas, Santa Clara, Cuba
e-mail: rbellop@uclv.edu.cu
Emilio S. Corchado, University of Salamanca, Salamanca, Spain
e-mail: escorchado@usal.es
Hani Hagras, University of Essex, Colchester, UK
e-mail: hani@essex.ac.uk
László T. Kóczy, Széchenyi István University, Győr, Hungary
e-mail: koczy@sze.hu
Vladik Kreinovich, University of Texas at El Paso, El Paso, USA
e-mail: vladik@utep.edu
Chin-Teng Lin, National Chiao Tung University, Hsinchu, Taiwan
e-mail: ctlin@mail.nctu.edu.tw
Jie Lu, University of Technology, Sydney, Australia
e-mail: Jie.Lu@uts.edu.au
Patricia Melin, Tijuana Institute of Technology, Tijuana, Mexico
e-mail: epmelin@hafsamx.org
Nadia Nedjah, State University of Rio de Janeiro, Rio de Janeiro, Brazil
e-mail: nadia@eng.uerj.br
Ngoc Thanh Nguyen, Wroclaw University of Technology, Wroclaw, Poland
e-mail: Ngoc-Thanh.Nguyen@pwr.edu.pl
Jun Wang, The Chinese University of Hong Kong, Shatin, Hong Kong
e-mail: jwang@mae.cuhk.edu.hk
More information about this series at http://www.springer.com/series/11156

Mohd Saberi Mohamad Miguel Rocha
•
Juan F. De Paz Tiago Pinto

•
Editors
11th International Conference

on Practical Applications
of Computational Biology
& Bioinformatics
123
Editors
Florentino Fdez-Riverola Juan F. De Paz
Escuela Superior de Ingeniería Informática Departamento de Informática y Automática
Universidad de Vigo Universidad de Salamanca
Ourense Salamanca
Spain Spain
Mohd Saberi Mohamad Tiago Pinto

Faculty of Computing Departamento de Informática y Automática
Universiti Teknologi Malaysia Universidad de Salamanca
Johor Salamanca
Malaysia Spain
Miguel Rocha
Department de Informática
Universidade do Minho
Braga
Portugal
ISSN 2194-5357 ISSN 2194-5365 (electronic)

Advances in Intelligent Systems and Computing
ISBN 978-3-319-60815-0 ISBN 978-3-319-60816-7 (eBook)
DOI 10.1007/978-3-319-60816-7
Library of Congress Control Number: 2017943012
© Springer International Publishing AG 2017

This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part
of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations,
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Printed on acid-free paper
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The registered company is Springer International Publishing AG
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
Preface
Biological and biomedical researches are increasingly driven by experimental

techniques that challenge our ability to analyze, process, and extract meaningful
knowledge from the underlying data. The impressive capabilities of next-generation
sequencing technologies, together with novel and ever-evolving distinct types of
omics data technologies, have put an increasingly complex set of challenges for the
growing fields of bioinformatics and computational biology. To address the mul-
tiple related tasks, for instance in biological modeling, there is the need to, more
than ever, create multidisciplinary networks of collaborators, spanning computer
scientists, mathematicians, biologists, doctors, and many others.
The International Conference on Practical Applications of Computational
Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to
emerging and challenging applied research in bioinformatics and computational
biology. Building on the success of previous events, the 11th edition of PACBB
Conference will be held on June 21–23, 2017, in the Polytechnic of Porto, Porto
(Portugal). In this occasion, special issues will be published by the Interdisciplinary
Sciences-Computational Life Sciences, Journal of Integrative Bioinformatics,
Neurocomputing, Journal of Computer Methods and Programs in Biomedicine,
Knowledge and Information Systems: An International Journal covering extended
versions of selected articles.
This volume gathers the accepted contributions for the 11th edition of the
PACBB Conference after being reviewed by different reviewers, from an interna-
tional committee from 13 countries. PACBB’17 technical program includes 39
papers of 61 submissions spanning many different subfields in bioinformatics and
computational biology.
Therefore, this event will strongly promote the interaction of researchers from
diverse fields and distinct international research groups. The scientific content will
be challenging and will promote the improvement of the valuable work that is being
carried out by the participants. In addition, it will promote the education of young
scientists, in a postgraduate level, in an interdisciplinary field.
We would like to thank all the contributing authors and sponsors, as well as the
members of the Program Committee and the Organizing Committee for their hard
v
vi Preface
and highly valuable work and support. Their effort has helped to contribute to the
success of the PACBB’17 event. PACBB’17 would not exist without your
assistance.
Mohd Saberi Mohamad

Miguel P. Rocha
Juan F. De Paz
PACBB’17 Programme Co-chairs
Tiago Pinto
PACBB’17 Organizing Co-chairs
Organization
General Co-chairs
Mohd Saberi Mohamad Universiti Teknologi Malaysia

Miguel Rocha University of Minho, Portugal
Juan F. De Paz University of Salamanca, Spain
Tiago Pinto University of Salamanca, Spain
Florentino Fdez-Riverola University of Vigo, Spain
Program Committee
Alejandro F. Villaverde IIM-CSIC, Spain

Alexandre Perera Lluna Universitat Politècnica de Catalunya, Spain
Alfonso Rodriguez-Paton Universidad Politecnica de Madrid, Spain
Alfredo Vellido Alcacena UPC, Spain
Alicia Troncoso University Pablo de Olavide, Spain
Amin Shoukry Egypt-Japan University of Science
and Technology, Egypt
Amparo Alonso University of A Coruña, Spain
Ana Cristina Braga University of Minho, Portugal
Ana Margarida Sousa University of MInho, Portugal
Anália Lourenço University of Vigo, Spain
Armando Pinho University of Aveiro, Portugal
Boris Brimkov Rice University, USA
Carlos A.C. Bastos University of Aveiro, Portugal
Carole Bernon IRIT/UPS, France
Carolyn Talcott Stanford University, USA
Daniel Glez-Peña University of Vigo, Spain
vii
viii Organization
David Hoksza Charles University in Prague,

Czech Republic
David Rodríguez Penas IIM-CSIC, Spain
Eduardo Valente IPCB, Spain
Eva Lorenzo Iglesias University of Vigo, Spain
Fernanda Brito Correia University of Aveiro, Portugal
Fernando De la Prieta University of Salamanca, Spain
Fernando Diaz-Gómez University of Valladolid, Spain
Filipe Liu University of Minho, Portugal
Francisco Couto University of Lisboa, Portugal
Gabriel Villarrubia University of Salamanca, Spain
Gael Pérez Rodríguez University of Vigo, Spain
Giovani Librelotto Federal University of Santa Maria, Brasil
Gustavo Isaza University of Caldas, Colombia
Gustavo Santos-García University of Salamanca, Spain
Hugo López-Fernández University of Vigo, Spain
Isabel C. Rocha University of Minho, Portugal
Javier Bajo Technical University of Madrid, Spain
Javier De Las Rivas CSIC, Spain
João Ferreira University of Lisboa, Portugal
Joel P. Arrais DEI/CISUC University of Coimbra,
Portugal
Jorge Vieira IBMC, Porto, Portugal
José Antonio Castellanos Garzón University of Salamanca, Spain
José Luis Oliveira University of Aveiro, Portugal
Josep Gómez Universitat Rovira i Virgili, Spain
Juan Ramos University of Salamanca, Spain
Julio R. Banga IIM-CSIC, Spain
Loris Nanni University of Bologna, Italy
Lourdes Borrajo Diz University of Vigo, Spain
Luis F. Castillo University of Caldas, Colombia
Luis M. Rocha Indiana University, USA
Mª Araceli Sanchís de Miguel University of Carlos III, Spain
Manuel Álvarez Díaz University of A Coruña, Spain
Marcelo Maraschin Federal University of Santa Catarina,
Florianopolis, Brazil
Marcos Martinez-Romero Stanford University, UK
Maria Olivia Pereira IBB - CEB Centre of Biological
Engineering, Portugal
Martin Krallinger CNIO, Spain
Martín Pérez-Pérez University of Vigo, Spain
Masoud Daneshtalab University of Turku, Finland
Miguel Reboiro University of Vigo, Spain
Mohd Firdaus Raih National University of Malaysia, Malaysia
Narmer Galeano Cenicafé, Colombia
Organization ix
Nuno F. Azevedo University of Porto, Portugal

Nuno Fonseca CRACS/INESC, Porto, Portugal
Oscar Dias CEB/IBB, Universidade do Minho, Portugal
Pablo Chamoso University of Salamanca, Spain
Patricia González University of A Coruña, Computer
Architecture Group (GAC), Spain
Paula Jorge IBB - CEB Centre of Biological
Engineering, Portugal
Pedro G. Ferreira Ipatimup - Institute of Molecular Pathology
and Immunology of the University
of Porto, Portugal
Pierpaolo Vittorini University of L’Aquila, Italy
Ramón Doallo University of A Coruña, Spain
René Alquezar Mancho UPC, Spain
Rita Ascenso Polytechnic Institute of Leiria, Portugal
Rita Margarida Teixeira Ascenso ESTG – IPL, Portugal
Rosalía Laza University of Vigo, Spain
Rui Camacho University of Porto, Portugal
Sara C. Madeira IST/INESC ID, Lisbon, Portugal
Sara Rodríguez University of Salamanca, Spain
Sérgio Deusdado Polytecnic Institute of Bragança, Portugal
Sergio Matos DETI/IEETA, Portugal
Thierry Lecroq University of Rouen, France
Valentin Brimkov SUNY Buffalo State College, USA
Vera Afreixo University of Aveiro, Portugal
Yingbo Cui National University of Defense Technology,
China
Organising Committee
Diogo Martinho Polytechnic of Porto, Portugal

Filipe Sousa Polytechnic of Porto, Portugal
João Soares Polytechnic of Porto, Portugal
Luís Conceição Polytechnic of Porto, Portugal
Nuno Borges Polytechnic of Porto, Portugal
Sérgio Ramos Polytechnic of Porto, Portugal
x Organization
PACBB 2016 Sponsors

Contents
S2P: A Desktop Application for Fast and Easy Processing

of 2D-Gel and MALDI-Based Mass Spectrometry Protein Data . . . . . . . 1
Hugo López-Fernández, Jose E. Araújo, Daniel Glez-Peña,
Miguel Reboiro-Jato, Florentino Fdez-Riverola,
and José L. Capelo-Martínez
Multi-Enzyme Pathway Optimisation Through Star-Shaped
Reachable Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Stanislav Mazurenko, Jiri Damborsky, and Zbynek Prokop
Automated Collection and Sharing of Adaptive Amino Acid
Changes Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Noé Vázquez, Cristina P. Vieira, Bárbara S.R. Amorim, André Torres,
Hugo López-Fernández, Florentino Fdez-Riverola, José L.R. Sousa,
Miguel Reboiro-Jato, and Jorge Vieira
ROC632: An Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Catarina Santos and Ana Cristina Braga
Processing 2D Gel Electrophoresis Images for Efficient
Gaussian Mixture Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Michal Marczyk
Improving Document Prioritization for Protein-Protein Interaction
Extraction Using Shallow Linguistics and Word Embeddings . . . . . . . . . 43
Sérgio Matos
K-Means Clustering with Infinite Feature Selection
for Classification Tasks in Gene Expression Data . . . . . . . . . . . . . . . . . . 50
Muhammad Akmal Remli, Kauthar Mohd Daud, Hui Wen Nies,
Mohd Saberi Mohamad, Safaai Deris, Sigeru Omatu, Shahreen Kasim,
and Ghazali Sulong
xi
xii Contents
Classification of Colorectal Cancer Using Clustering and Feature

Selection Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Hui Wen Nies, Kauthar Mohd Daud, Muhammad Akmal Remli,
Mohd Saberi Mohamad, Safaai Deris, Sigeru Omatu, Shahreen Kasim,
and Ghazali Sulong
Development of Text Mining Tools for Information Retrieval
from Patents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Tiago Alves, Rúben Rodrigues, Hugo Costa, and Miguel Rocha
How Can Photo Sharing Inspire Sharing Genomes? . . . . . . . . . . . . . . . . 74
Vinicius V. Cogo, Alysson Bessani, Francisco M. Couto,
Margarida Gama-Carvalho, Maria Fernandes,
and Paulo Esteves-Verissimo
An App Supporting the Self-management of Tinnitus . . . . . . . . . . . . . . . 83
Chamoso Pablo, De La Prieta Fernando, Eibenstein Alberto, Tizio Angelo,
and Vittorini Pierpaolo
Anthropometric Data Analytics: A Portuguese Case Study . . . . . . . . . . . 92
António Barata, Lucília Carvalho, and Francisco M. Couto
Reverse Inference in Symbolic Systems Biology . . . . . . . . . . . . . . . . . . . . 101
Beatriz Santos-Buitrago, Adrián Riesco, Merrill Knapp,
Gustavo Santos-García, and Carolyn Talcott
Skin Temperature Monitoring to Avoid Foot Lesions
in Diabetic Patients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
A. Queiruga-Dios, J. Bullón Pérez, A. Hernández Encinas,
J. Martín-Vaquero, A. Martínez Nova, and J. Torreblanca González
Multidimensional Feature Selection and Interaction Mining
with Decision Tree Based Ensemble Methods . . . . . . . . . . . . . . . . . . . . . . 118
Lukasz Krol and Jonna Polanska
A Normalisation Strategy to Optimally Design Experiments
in Computational Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Míriam R. García, Antonio A. Alonso, and Eva Balsa-Canto
Mitosis Detection in Breast Cancer Using Superpixels
and Ensemble Classifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
César A. Ortiz Toro, Consuelo Gonzalo Martín, Angel García Pedrero,
Alejandro Rodriguez Gonzalez, and Ernestina Menasalvas
Reproducibility of Finding Enriched Gene Sets in Biological
Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Joanna Zyla, Michal Marczyk, and Joanna Polanska
Contents xiii
Towards Trustworthy Predictions of Conversion from Mild Cognitive

Impairment to Dementia: A Conformal Prediction Approach . . . . . . . . . 155
Telma Pereira, Sandra Cardoso, Dina Silva, Alexandre de Mendonça,
Manuela Guerreiro, and Sara C. Madeira
Topological Sequence Segments Discriminate Between Class
C GPCR Subtypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Caroline König, René Alquézar, Alfredo Vellido, and Jesús Giraldo
QmihR: Pipeline for Quantification of Microbiome in Human
RNA-seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Bruno Cavadas, Joana Ferreira, Rui Camacho, Nuno A. Fonseca,
and Luisa Pereira
Improving Prognostic Prediction from Mild Cognitive Impairment
to Alzheimer’s Disease Using Genetic Algorithms . . . . . . . . . . . . . . . . . . 180
Francisco L. Ferreira, Sandra Cardoso, Dina Silva, Manuela Guerreiro,
Alexandre de Mendonça, and Sara C. Madeira
Novel Method of Identifying DNA Methylation Fingerprint
of Acute Myeloid Leukaemia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Agnieszka Cecotka and Joanna Polanska
Metadata Analyser: Measuring Metadata Quality . . . . . . . . . . . . . . . . . . 197
Bruno Inácio, João D. Ferreira, and Francisco M. Couto
Vascular Contraction Model Based on Multi-agent Systems . . . . . . . . . . 205
J.A. Rincon, Guerra-Ojeda Sol, V. Julian, and C. Carrascosa
Study of the Epigenetic Signals in the Human Genome . . . . . . . . . . . . . . 213
Susana Ferreira, Vera Afreixo, Gabriela Moura, and Ana Tavares
Cloud-Assisted Read Alignment and Privacy . . . . . . . . . . . . . . . . . . . . . . 220
Maria Fernandes, Jérémie Decouchant, Francisco M. Couto,
and Paulo Esteves-Verissimo
On the Role of Inverted Repeats in DNA Sequence Similarity . . . . . . . . 228
Morteza Hosseini, Diogo Pratas, and Armando J. Pinho
An Ensemble Approach for Gene Selection in Gene
Expression Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
José A. Castellanos-Garzón, Juan Ramos, Daniel López-Sánchez,
and Juan F. de Paz
Dissimilar Symmetric Word Pairs in the Human Genome . . . . . . . . . . . 248
Ana Helena Tavares, Jakob Raymaekers, Peter J. Rousseeuw,
Raquel M. Silva, Carlos A.C. Bastos, Armando Pinho, Paula Brito,
and Vera Afreixo
xiv Contents
A Critical Evaluation of Automatic Atom Mapping Algorithms

and Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Nuno Osório, Paulo Vilaça, and Miguel Rocha
Substitutional Tolerant Markov Models for Relative Compression
of DNA Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Diogo Pratas, Morteza Hosseini, and Armando J. Pinho
Biomedical Word Sense Disambiguation with Word Embeddings. . . . . . 273
Rui Antunes and Sérgio Matos
Classification Tools for Carotenoid Content Estimation in Manihot
esculenta via Metabolomics and Machine Learning . . . . . . . . . . . . . . . . . 280
Rodolfo Moresco, Telma Afonso, Virgílio G. Uarrota,
Bruno Bachiega Navarro, Eduardo da C. Nunes, Miguel Rocha,
and Marcelo Maraschin
UV-Vis Spectrophotometry and Chemometrics as Tools for
Recognition of the Biochemical Profiles of Organic Banana
Peels (Musa sp.) According to the Seasonality in Southern Brazil. . . . . . 289
Susane Lopes, Rodolfo Moresco, Luiz Augusto Martins Peruch,
Miguel Rocha, and Marcelo Maraschin
Influence of Solar Radiation on the Production of Secondary
Metabolites in Three Rice (Oryza sativa) Cultivars . . . . . . . . . . . . . . . . . . 297
Eva Regina Oliveira, Ester Wickert, Fernanda Ramlov, Rodolfo Moresco,
Larissa Simão, Bruno B. Navarro, Claudia Bauer, Débora Cabral,
Miguel Rocha, and Marcelo Maraschin
Cryfa: A Tool to Compact and Encrypt FASTA Files . . . . . . . . . . . . . . . 305
Diogo Pratas, Morteza Hosseini, and Armando J. Pinho
An Automated Colourimetric Test by Computational
Chromaticity Analysis: A Case Study of Tuberculosis Test . . . . . . . . . . . 313
Marzia Hoque Tania, K.T. Lwin, Kamal AbuHassan,
Noremylia Mohd Bakhori, Umi Zulaikha Mohd Azmi, Nor Azah Yusof,
and M.A. Hossain
Characterization of the Chemical Composition of Banana Peels
from Southern Brazil Across the Seasons Using Nuclear Magnetic
Resonance and Chemometrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch,
Miguel Rocha, and Aline Pereira
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
S2P: A Desktop Application for Fast and Easy
Processing of 2D-Gel and MALDI-Based Mass
Spectrometry Protein Data
Hugo López-Fernández1,2,3 ✉ , Jose E. Araújo3, Daniel Glez-Peña1,2,

( )
Miguel Reboiro-Jato , Florentino Fdez-Riverola1,2, and José L. Capelo-Martínez3

1,2
1
ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidad de Vigo,
Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
{hlfernandez,dgpena,mrjato,riverola}@uvigo.es
2
CINBIO - Centro de Investigaciones Biomédicas, University of Vigo,
Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
3
UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia,
Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
{jeduardoaraujo,jlcapelom}@bioscopegroup.org
Abstract. 2D-gel electrophoresis is widely used in combination with MALDI-

TOF mass spectrometry in order to analyse the proteome of biological samples.
It can be used to discover proteins that are differentially expressed between two
groups (e.g. two disease conditions) obtaining thus a set of potential biomarkers.
Biomarker discovery requires a lot of data processing in order to prepare data for
analysis or in order to merge data from different sources. This kind of work is
usually done manually, being highly time consuming and distracting the operator
or researcher from other important tasks. Moreover, doing this repetitive process
in a non-automated, handling-based manner is error-prone, affecting reliability
and reproducibility. To overcome these drawbacks, the S2P, an AIBench based
desktop multiplatform application, has been specifically created to process 2D-
gel and MALDI-mass spectrometry protein identification-based data in a
computer-aided manner. S2P is open source and free to all users at http://www.
sing-group.org/s2p.
Keywords: Protein identification · Data processing · Bioinformatics tools · Open

source · 2D-gel · MALDI-TOF-MS · Protein data · Mascot identifications
1 Introduction
2D-gel electrophoresis and mass spectrometry using matrix assisted laser desorption
ionization coupled to time of flight analysers, MALDI-TOF-MS, are widely used in
conjunction in order to perform proteome analysis [1, 2]. In brief, while the comparison
of 2D-gels allows obtaining a set of differentially expressed spots, MALDI-TOF-MS
allows to identify the proteins separated in such spots.
© Springer International Publishing AG 2017

F. Fdez-Riverola et al. (eds.), 11th International Conference on Practical
Applications of Computational Biology & Bioinformatics, Advances in Intelligent
Systems and Computing 616, DOI 10.1007/978-3-319-60816-7_1
2 H. López-Fernández et al.
The scientific community is particularly interested in the challenging task of finding

proteins that can be used to differentiate different conditions of health with the aim to
aid in diagnosis, prognosis and new targeted therapies development [3–5]. In order to
find such proteins, known as biomarkers, a typical experimental workflow combining
2D-gel and MALDI-TOF-MS can involve the following steps: (i) separation of the
proteins present in a complex proteome; (ii) comparing the 2D-gels across samples to
obtain the spots that were found expressed differentially; (iii) excising such spots and
treating them for protein identification; (iv) linking the protein identifications to the 2D-
gel spots; and (v) performing different types of data analysis to find out the potential
biomarkers. Such workflow generates a large amount of data, which need to be processed
before it can be properly analysed. A considerable part of the aforementioned data
processing is usually carried out manually by laboratory researchers (e.g. using text
editors and Excel). However, doing this repetitive process in a non-automated way
presents important drawbacks: it is time consuming, it is error-prone, and it tends to lack
reliability and reproducibility.
To overcome the aforementioned drawbacks we have developed the S2P software
application (http://www.sing-group.org/s2p/), a free software that aims to help
researchers overcoming these tedious but necessary data processing steps.
S2P has been created with two main goals in mind: to improve reproducibility and
to save time. Nowadays, lack of reproducibility is a growing concern in science [6] and
the S2P software aims to improve reproducibility by avoiding human errors due to
manual data processing. For instance, this issue has been particularly important in recent
genomics bioinformatics, where it has been demonstrated that gene name errors are
widespread in the scientific literature due to the use of Excel [7, 8]. Through its user-
friendly GUI interface, S2P dramatically reduces the time that researchers need to invest
in order to get data ready for analysis. The usefulness of S2P is illustrated by a case
study experiment that aims to establish a biomarker-based method to allow better diag‐
nosis and monitoring of patients with bladder cancer.
The rest of the paper is structured as follows. Section 2 presents the case study and
the most relevant implementation details. Section 3 reviews the results, showing how
to use S2P to process the case study dataset. Finally, Sect. 4 concludes the paper and
outlines future research work.
2 Materials and Methods
2.1 Case Study
As a case study, a dataset composed by 14 patients plus 1 healthy group of 6 individuals

was used. Plasma samples from 7 anonymous patients diagnosed with bladder cancer,
7 anonymous patients diagnosed with lower urinary tract symptoms (LUTS) and 6
healthy individuals were collected following standard procedures. Both patients and
healthy volunteers were informed about the project and their consent was obtained in
written form. The local ethics committee approved the study. This experiment was
developed as a proof of concept to differentiate bladder cancer from LUTS.
S2P: A Desktop Application for Fast and Easy Processing 3
Once in the laboratory, the samples were centrifuged, and then the supernatant was
withdrawn, aliquoted and stored at –80 °C until analysis. Most abundant proteins
(MAPs) in plasma can mask or interfere with the detection of proteins belonging to the
low-abundance protein fraction [9]. To avoid this problem, protein equalization from
plasma samples was performed with dithiothreitol, DTT, according to the protocol
described by Warder et al. [10] with minor modifications as described by Fernández
et al. [11] and Araújo et al. [12–14]. This process was performed with five replicates for
each patient. Then, the total protein content was determined using a Bradford protein
assay [15].
Two dimensional gel electrophoresis separation was carried out by duplicate for each
patient and for the healthy pool. Then, 2D-gels obtained for each patient and the pool
of healthy volunteers were compared using the Progenesis SameSpots software v4.0
(NonLinear Dynamics) to find out the differentially expressed proteins. All spots of
interest were excised and subjected to in-gel protein(s) digestion and then to protein
fingerprint identification by mass spectrometry using MALDI-TOF-MS [16]. Finally,
S2P was used to process the spots data (i.e. differentially expressed spots) obtained with
the SameSpots software as well as to analyze them along with the protein identifications
obtained from Mascot.
2.2 Implementation
S2P v1.0.0 is implemented in Java and it was constructed using the AIBench framework
[17], which has been demonstrated to be suitable for rapid development of scientific
applications [18, 19]. The Graphical User Interface (GUI) was constructed in Java Swing
using freely available extensions such as SwingX or GC4S. S2P also makes use of several
well-established open-source libraries such as JFreeChart, charts4j, iText and the
Apache Commons Mathematics library.
The source code of the project is freely available at https://github.com/sing-
group/S2P under a GNU GPL 3.0 License (http://www.gnu.org/copyleft/gpl.html). It is
divided into three modules: (i) core, which contains the default implementation API, (ii)
gui, which contains several reusable GUI components, and (iii) aibench, which contains
a GUI application based on the AIBench framework.
3 Results and Discussion
With the goal of showing the main features of S2P as well as its usefulness to analyse
real data, this section shows how it has been used to process and analyse the case study
data presented.
Figure 1 illustrates the five main steps where S2P was used through the experiments:
(1) to merge the SameSpots report into a single table where all samples can be compared;
(2) to design the MALDI plate; (3) to load and filter the Mascot identifications; (4) to
link the Mascot identifications with their corresponding spots using the MALDI plate;
and (5) to examine and analyse spots data along with Mascot identifications. All data
needed to reproduce the steps explained below is available at http://www.sing-

group.org/s2p/tutorial.html, along with a detailed quick-start tutorial that guides users
using S2P for the first time.
Fig. 1. Schematic S2P flow diagram.
The case study dataset was composed by 7 anonymous patients diagnosed with
bladder cancer, 7 anonymous patients diagnosed with lower urinary tract symptoms
(LUTS) and 6 healthy individuals that were pooled. The Progenesis SameSpots software
was used to compare the 2D-gels corresponding to each individual against the health
pool’s 2D-gels to obtain the differentially expressed spots. These results were exported
using the “Export report” option of SameSpots, which creates one HTML file per
comparison (i.e. 14 files in this case). S2P was then used to parse and merge these reports
into a single table with samples in columns and spots in rows (Step 1 of Fig. 1). This
table was exported into a comma-separated values (CSV) file that can be easily reopen
with S2P as well as external applications such as Excel, LibreOffice or R.
Then, these differentially expressed spots were first treated and then analysed
through MALDI-TOF MS in order to identify their protein content. To do that, a dedi‐
cated sample treatment is done [16] and the pool of peptides obtained is spotted twice
into a MALDI plate, which is then introduced into the MALDI apparatus for analysis.
Usually, researchers fill a sheet with the position of the spots in the plate so that they
can trace back where each spot was placed. This is important to know which spot is
associated to each MALDI spectrum and, therefore, to know which Mascot identifica‐
tions are associated to each spot. However, keeping a unique handwritten copy of this
key information is risky as it can be lost or mislead and, most likely, it will be no way
to recover this information. For these two reasons, S2P incorporates a MALDI plate
editor that allows the storage of digital copies of experiments’ plates as well as print
them into PDF files (Step 2 of Fig. 1). S2P also allows to automatically filling the plate
using a set of previously loaded spots (Step 1 of Fig. 1), allowing the user to define
parameters such as matrix dimensions (i.e. number of rows and columns) or the number
of replicates of each spot. In our case study, S2P was used to create the MALDI plate
and to obtain a printed copy of it that is used to guide the experimental work.
Once the MALDI-TOF MS analysis was done, the MALDI-based spectra of the
digested protein(s) were submitted to Mascot in order to identify the proteins. Then,
they were exported into a HTML file that was loaded into S2P in order to remove dupli‐
cated entries and exclude identifications with a Mascot score under 56 (Step 3 of Fig. 1).
This processed list of Mascot identifications was exported into a CSV file so that it can
be directly loaded into S2P later or used in other applications (e.g. Excel). Then, these
Mascot identifications integrated with the spots data using the MALDI plate (Step 4 of
Fig. 1) to know which identifications are associated with each spot.
Finally (Step 5 of Fig. 1), S2P allows an integrated analysis of the spots data and the
Mascot identifications (Fig. 2). In the context of our case study, this option was firstly
used to try to identify potential biomarkers of the two conditions of interest. When the
healthy pool was compared with the bladder cancer patients, four differentially expressed
spots present in at least 5 of 7 bladder cancer patients (Fig. 3A) were found. The corre‐
sponding proteins were: (i) Serum albumin (Spot Number [SN] = 137), (ii) Gelsolin
(SN = 137), (iii) Fibrinogen gamma chain (SN = 337), (iv) Ig alpha-1 chain C region
(SN = 360), (v) Ig alpha-2 chain C region (SN = 360) and (vi) Haptoglobin (SN = 266).
When the healthy pool was compared with the LUTS patients, we found five differen‐
tially expressed spots that were present in at least 4 of 7 LUTS patients (Fig. 3B). The
associated proteins were the following: (i) CD5 antigen-like (SN = 244), (ii) Heparin
cofactor 2 (SN = 175 and SN = 190), (iii) Hemopexin (SN = 175), (iv) Serum albumin
(SN = 192 and SN = 190) and (v) Inter-alpha-trypsin inhibitor heavy chain H4 (SN = 88).
Fig. 2. Screenshot of the S2P integrated analysis window.

Fig. 3. Heat maps showing the differentially expressed spots.
As it can be seen in Fig. 3, a small set of candidate biomarkers was identified that
can be associated to each disease. Due to this reason, a complementary approach was
experimented: exporting all spots data from Samespots instead of exporting only those
spots that were differentially expressed when each individual and the healthy pool were
compared. This way, we used S2P to process these new dataset (analogously to step 1)
and then to find spots whose average value were statistically different between bladder
cancer and LUTS patients. Following this strategy, 40 differentially expressed spots (i.e.
having t-test p-values corrected using Benjamini-Hochberg less than 0.05) between
bladder cancer and LUTS were found, 27 of which have protein identifications associ‐
ated (corresponding to 14 unique proteins). This also allowed us to compare the distri‐
bution of the expression values of each condition using box plots. For instance, Fig. 4
shows the box plots of the two spots identified in Fig. 3 that are differentially expressed
between bladder cancer and LUTS patients. This information must be carefully
analysed, but the usefulness of S2P to fast and accurate process and analyse data is thus
proven.
Finally, it is important to remark that doing the steps described above manually took
more than two weeks of handling. Now, with the help of S2P this data processing time
Fig. 4. Box plots of the differentially expressed spots.

has been dramatically reduced to a few minutes. Moreover, S2P offers the additional
data analysis features shown that also allow researchers saving a lot of their valuable
time.
4 Conclusions
S2P (http://www.sing-group.org/s2p/) is freely distributed under license GPLv3,

providing a friendly graphical user interface designed to allow researchers saving time
in data processing tasks related to 2D-gel electrophoresis and MALDI mass spectrom‐
etry protein identification-based data. The usefulness of S2P has been demonstrated by
its application to a real experiment, where it notably speed up data processing as well
as it improves experiment reproducibility and reliability. S2P is open to further exten‐
sions and we are currently developing support for more types of datasets.
Acknowledgements. This work has been partially funded by (i) the “Platform of integration of
intelligent techniques for analysis of biomedical information” project (TIN2013-47153-C3-3-R)
from Spanish Ministry of Economy and Competitiveness, (ii) the “Discovery of biomarkers for
bladder carcinoma diagnosis” project from Nova Medical School, (iii) Unidade de Ciências
Biomoleculares Aplicadas-UCIBIO, which is financed by national funds from FCT/MEC/
Portugal (UID/Multi/04378/2013), and (iv) Consellería de Cultura, Educación e Ordenación
Universitaria (Xunta de Galicia) and FEDER (European Union). H. López-Fernández is supported
by a post-doctoral fellowship from Xunta de Galicia. J. L. Capelo acknowledges Associação
Cientifica ProteoMass for financial support. J. E. Araújo acknowledges the financial support given
by the Portuguese Foundation for Science and Technology under doctoral grant number
SFRH/BD/109201/2015. SING group thanks CITI (Centro de Investigación, Transferencia e
Innovación) from University of Vigo for hosting its IT infrastructure.
References
1. Susnea, I., Bernevic, B., Wicke, M., Ma, L., Liu, S., Schellander, K., Przybylski, M.:
Application of MALDI-TOF-Mass spectrometry to proteome analysis using stain-free gel
electrophoresis. In: Cai, Z., Liu, S. (eds.) Applications of MALDI-TOF Spectroscopy, pp. 37–
54. Springer, Heidelberg (2012)
2. Martinez, J.L.C., Espiño, C.L., Santos, H.M.: Mass spectrometry-based proteomics: what is
it expecting ahead? J. Proteomics 145, 1–2 (2016)
3. Nagalla, S.R., Canick, J.A., Jacob, T., Schneider, K.A., Reddy, A.P., Thomas, A., Dasari, S.,
Lu, X., Lapidus, J.A., Lambert-Messerlian, G.M., Gravett, M.G., Roberts, C.T., Luthy, D.,
Malone, F.D., D’Alton, M.E.: Proteomic analysis of maternal serum in down syndrome:
identification of novel protein biomarkers. J. Proteome Res. 6, 1245–1257 (2007)
4. Thongboonkerd, V., Mcleish, K.R., Arthur, J.M., Klein, J.B.: Proteomic analysis of normal
human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int.
62, 1461–1469 (2002)
5. Hsueh, C.-T., Liu, D., Wang, H.: Novel biomarkers for diagnosis, prognosis, targeted therapy
and clinical trials. Biomark. Res. 1, 1 (2013)
6. Baker, M.: Reproducibility: Seek out stronger science. Nature 537, 703–704 (2016)
7. Zeeberg, B.R., Riss, J., Kane, D.W., Bussey, K.J., Uchio, E., Linehan, W.M., Barrett, J.C.,
Weinstein, J.N.: Mistaken Identifiers: Gene name errors can be introduced inadvertently when
using Excel in bioinformatics. BMC Bioinformatics 5, 80 (2004)
8. Ziemann, M., Eren, Y., El-Osta, A.: Gene name errors are widespread in the scientific
literature. Genome Biol. 17 (2016)
9. Anderson, N.L.: The Human Plasma Proteome: History, Character, and Diagnostic Prospects.
Mol. Cell. Proteomics 1, 845–867 (2002)
10. Warder, S.E., Tucker, L.A., Strelitzer, T.J., McKeegan, E.M., Meuth, J.L., Jung, P.M., Saraf,
A., Singh, B., Lai-Zhang, J., Gagne, G., Rogers, J.C.: Reducing agent-mediated precipitation
of high-abundance plasma proteins. Anal. Biochem. 387, 184–193 (2009)
11. Fernández, C., Santos, H.M., Ruíz-Romero, C., Blanco, F.J., Capelo-Martínez, J.-L.: A
comparison of depletion versus equalization for reducing high-abundance proteins in human
serum. Electrophoresis 32, 2966–2974 (2011)
12. Araújo, J.E., Santos, T., Jorge, S., Pereira, T.M., Reboiro-Jato, M., Pavón, R., Magriço, R.,
Teixeira-Costa, F., Ramos, A., Santos, H.M.: Matrix-assisted laser desorption/ionization time-
of-flight mass spectrometry-based profiling as a step forward in the characterization of
peritoneal dialysis effluent. Anal. Methods 7, 7467–7473 (2015)
13. Araújo, J.E., Jorge, S.: Teixeira e Costa, F., Ramos, A., Lodeiro, C., Santos, H.M., Capelo,
J.L.: A cost-effective method to get insight into the peritoneal dialysate effluent proteome. J.
Proteomics 145, 207–213 (2016)
14. Araújo, J.E., Jorge, S., Magriço, R., Costa, T.E, Ramos, A., Reboiro-Jato, M., Fdez-Riverola,
F., Lodeiro, C., Capelo, J.L., Santos, H.M.: Classifying patients in peritoneal dialysis by mass
spectrometry-based profiling. Talanta 152, 364–370 (2016)
15. Bradford, M.M.: A rapid and sensitive method for the quantitation of microgram quantities
of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976)
16. Oliveira, E., Araújo, J.E., Gómez-Meire, S., Lodeiro, C., Perez-Melon, C., Iglesias-Lamas,
E., Otero-Glez, A., Capelo, J.L., Santos, H.M.: Proteomics analysis of the peritoneal dialysate
effluent reveals the presence of calcium-regulation proteins and acute inflammatory response.
Clin. Proteomics 11, 17 (2014)
17. Glez-Peña, D., Reboiro-Jato, M., Maia, P., Rocha, M., Díaz, F., Fdez-Riverola, F.: AIBench:
a rapid application development framework for translational research in biomedicine.
Comput. Methods Programs Biomed. 98, 191–203 (2010)
18. López-Fernández, H., Reboiro-Jato, M., Glez-Peña, D., Méndez Reboredo, J.R., Santos, H.M.,
Carreira, R.J., Capelo-Martínez, J.L., Fdez-Riverola, F.: Rapid development of Proteomic
applications with the AIBench framework. J. Integr. Bioinforma. 8, 171 (2011)
19. Reboiro-Jato, M., Glez-Peña, D., Méndez-Reboredo, J.R., Santos, H.M., Carreira, R.J.,
Capelo, J.L., Fdez-Riverola, F.: Building proteomics applications with the aibench application
framework (2011)
Multi-Enzyme Pathway Optimisation
Through Star-Shaped Reachable Sets
Stanislav Mazurenko1(B) , Jiri Damborsky1,2 , and Zbynek Prokop1,2

1
Faculty of Science, Research Centre for Toxic Compounds in the Environment
RECETOX, Loschmidt Laboratories, Masaryk University,
Kamenice 753/5, 625 00 Brno, Czech Republic
stan.mazurenko@gmail.com
2
St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
Abstract. This article studies the time evolution of multi-enzyme path-

ways. The non-linearity of the problem coupled with the infinite dimen-
sionality of the time-dependent input usually results in a rather laborious
optimization. Here we discuss how the optimization of the input enzyme
concentrations might be efficiently reduced to a calculation of reachable
sets. Under some general conditions, the original system has star-shaped
reachable sets that can be derived by solving a partial differential equa-
tion. This method allows a thorough study and optimization of quite
sophisticated enzymatic pathways with non-linear dynamics and possi-
ble inhibition. Moreover, optimal control synthesis based on reachable
sets can be implemented and was tested on several simulated examples.
Keywords: Enzyme kinetics, Optimal control, Synthetic biology,

Metabolic networks, Non-linear dynamics
1 Introduction
1.1 Multi-Enzyme Pathways
In this paper, we consider a set of chemical reactions catalysed by several
enzymes. Such reactions take place inside cells and are also used in synthetic
biology, e.g. in manufacturing of chemical compounds, biodegradation, medi-
cine, etc. Currently, there are large databases of enzymes based on which path-
ways can be constructed to turn given substrates into desired products [1]. The
enzyme kinetic optimisation of these processes is high on the agenda as it may
lead to a substantial economy of time and consumables. Such optimisation may
This research was supported by the National Sustainability Programme of the Czech
Ministry of Education, Youth and Sports (LO1214) and the RECETOX research
infrastructure (LM2011028).
Electronic supplementary material The online version of this chapter (doi:10.
1007/978-3-319-60816-7 2) contains supplementary material, which is available to
authorized users.

c Springer International Publishing AG 2017
F. Fdez-Riverola et al. (eds.), 11th International Conference on Practical
Applications of Computational Biology & Bioinformatics, Advances in Intelligent
Systems and Computing 616, DOI 10.1007/978-3-319-60816-7 2
10 S. Mazurenko et al.
also provide insights into the evolution of cells since some studies suggest that
optimal pathways are evolutionarily advantageous and can be predicted based
on the genetic information of living cells [2].
We consider an n-step chemical reaction in which the state variables are
the concentrations of metabolites produced and consumed in the course of the
reaction:
E0 E2 En−2 En−1
S −−→ M1 −−→ . . . −−−→ Mn−2 −−−→ P.
The control here are the concentrations of enzymes Ei , the sum of which is
limited from above. We will prove that under some general assumptions about
the rate equations, one can expect the set of all the possible states of such
systems to be star-shaped at any point in time. As a result, an optimisation of
the pathway using star-shaped reachable sets [3] can be implemented to obtain
the maximum concentration of the final product and the corresponding optimal
profile of enzymes.
1.2 Mathematical Setup

For a pathway consisting of n consecutive steps, we will use the following nota-
tions: ei is the concentration of the enzyme responsible for step i; xi is the
metabolite concentration; fi (x, t), x = (x1 , . . . , xn ), is the reaction rate per unit
of the enzyme concentration ei . We assume that fi includes all the individual
kinetic parameters such as kcat and KM and may depend on the concentrations
of all the metabolites involved (e.g., systems with cross-inhibition are included).
Moreover, the dependence of all the variables on t is implied in all the cases
below, but we will omit this explicit notation for the sake of simplicity. In prac-
tice, all the rates fi are non-linear, which significantly complicates any treatment
of such systems.
According to enzyme kinetics, the time evolution of a multi-enzyme system
over the time t ∈ [0, T ] can be described as follows:
⎧
⎪
⎪ ẋ1 = e0 f0 (x ) − e1 f1 (x ),
⎪
⎪
⎨ ẋ2 = e1 f1 (x ) − e2 f2 (x ),
... (1)
⎪
⎪
⎪
⎪ ẋn−1 = e f
n−2 n−2 (x ) − e f
n−1 n−1 (x ),
⎩
ẋn = en−1 fn−1 (x ).
In order to make sure that none of the concentrations becomes negative, we
will require that for any metabolite i the rate fi−1 is non-negative and fi is
non-positive at xi = 0. In other words, metabolite i is not consumed when its
concentration is already zero.
We will consider the following control set:

n−1

e ∈ E = (e0 , . . . , en−1 ) ei ≥ 0, i = 0..n − 1, ei ≤ Emax ,

i=0
which indicates that at any moment in time the total enzyme concentration
must not exceed a certain predefined value Emax . This limitation, for example,
Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets 11
describes limited resources of a cell that force it to choose which enzyme to

produce or maintain at any point in time.
As far as the starting points are concerned, we will consider the following
two most wide-spread frameworks: (A) all xi (0) = 0 and f0 ≥ 0 (there is a con-
stant supply of the initial substrate); or (B) the initial concentration x1 (0) = 1,
xi (0) = 0 for i = 2..n, and f0 ≡ 0 (the first metabolite is the initial substrate
being consumed in the course of the reaction).
Finally, we will assume that the standard existence and uniqueness results
hold for the solutions to (1) over the whole relevant time interval for any mea-
surable input ē ∈ E [4,5], which is usually the case in enzyme kinetics since the
state vector denotes real concentrations limited from above and below. We will
provide some examples of such systems in the following sections.
1.3 Optimal Control

In this framework, several objectives for optimal control are possible. Usually,
one is interested in maximizing the final product, which can be formulated either
as the minimization of the transition time tf to drive xn to some predefined
level [6] or by maximizing xn at a fixed point in time [7]. Other definitions of the
transition time are also possible [8–10]. Moreover, a multi-objective optimization
problem can also occur [11]. For the sake of simplicity, we will be considering
the maximization of the final product at a given point in time although more
general target functions can also be used (see below).
There are two main groups of methods commonly used to find optimal solu-
tions: the so-called direct and indirect methods. The former usually imply a
transformation of the original problem into non-linear programming by time-
discretization and approximation of the control variables either alone or together
with the states (for a comprehensive review see [11]). The advantages include a
great variety of solvers, a general applicability, and an intuitive implementation.
Nonetheless, these methods require some preliminary proof of the existence and
stability of the solution. Moreover, global optima finders are much more com-
putationally expensive than local ones, and due to the innate infinite dimen-
sionality, the costs of refining the grid are high. Finally, if the target function is
changed, e.g. to account for other metabolites, the entire calculation has to be
repeated.
The indirect methods suggest analytical treatment of the problem, e.g., by
using Pontryagin’s maximum principle [2,6,9,10]. The main advantages include
a more comprehensive analysis of the system behaviour and simpler numerical
methods. However, Pontryagin’s maximum principle is only a necessary condi-
tion, and the exact analytical solutions are usually difficult to obtain even in
the case of simple linear systems. The proof of a global maximum is again com-
plicated, and any change of the model, e.g. addition of cross-inhibition, may
completely invalidate the analysis.
In this article, we suggest an alternative indirect method based on exact
reachable sets [12,13], i.e. the states of a multi-enzyme system reachable from
the initial point for all the possible enzyme profiles. While this method is more
computationally intensive than the maximum principle, it provides the time-

evolution of the system in full since all the possible states are analysed. This
allows for some flexibility in choosing the target functional after the calculation
of reachable sets. Optimal control synthesis may be implemented in various ways
once the sets are calculated, and the global optimality is implied automatically.
No change to the model will require any qualitative re-analysis. Moreover, geo-
metric state constraints may be taken into account, which extends the applica-
bility of the method to, e.g. the problems with metabolite constraints due to
metabolite toxicity. Finally, given some relatively broad assumptions about the
reaction rates, the reachable sets are star-shaped, which reduces the problem
dimensionality by one and enhances its computational efficiency and applicabil-
ity. The summary table comparing the approaches mentioned above is given in
the Supplement (table S1).
2 Star-Shaped Reachable Sets

We will now briefly define reachable sets and their applications to optimization,
provide the evolution theorems for star-shaped sets, and formulate the main
theoretical result for the systems in question.
2.1 Reachable Sets and Optimization

Reachable sets provide an important tool for the analysis of the time evolution
of systems as they demonstrate how systems might behave given every possible
control input. In order to demonstrate a general idea, consider the following
differential inclusion:
ẋ ∈ F (t, x ), x (t0 ) ∈ X0 , t ∈ T = [t0 , t1 ], (2)
where X0 is a compact subset of Rn and F is a continuous multivalued map from
T × Rn to compact convex subsets of Rn . For instance, (1) can be formulated in
the above terms if one takes the union of the right-hand side of the equations over
e ∈ E. This differential equation generates a bundle of trajectories; consequently,
its behaviour may be translated into that of the bundle. Let the reachable set X[t]
be the set of all possible states of the system at time t. The intuitive strategy to
find X[t] by inserting different values from F (t, x ) may work only if an explicit
analytical solution is available, which is hardly ever the case even for linear
systems. However, under some general assumptions on F, the reachable set can
be found as the solution to an evolutionary equation [14]. While this equation
is usually difficult to solve, a great variety of methods has been developed to
calculate such sets [12,13,15].
In this paper, we will use the fact that under some general assumptions (see
the Supplement), inclusion 2 has reachable sets that are star-shaped [16,17], i.e.
they are compact, and for any λ ∈ [0, 1] the set λX[t] ⊆ X[t]. Such sets are
uniquely defined by their radial function:
r(l , t) = r(l |X[t]) = max{λ ≥ 0 : λl ∈ X[t]}
Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets 13
that is the viscosity solution to the following partial differential equation on an

n-dimensional sphere S n :

∂r ∂s r 1
=ρ − + rl F (t, rl ) , (3)
∂t ∂l r
where ρ(l |F ) = sup{ i li yi |y ∈ F } is the support function. This result, together

with viscosity methods [18,19], provides a powerful tool for an exact calculation
of reachable sets, e.g. for multi-enzyme reactions as demonstrated below.
As soon as one calculates the reachable set X[t], the optimal solution to
maximizing xn at time T is tantamount to finding the point in X[T ] with the
maximal value of coordinate xn . In general, any target function dependent only
on the final metabolite concentrations can be used since given X[T ], the initial
optimal control problem turns into a relatively simple optimization of the func-
tion over the set X[T ]. And once the optimal point has been found, one may
apply control synthesis strategies to find the control profile that will lead the
system to this optimum [3].
2.2 Star-Shaped Sets Generated by Multi-Enzyme Pathway

We will now apply the results of the previous subsection to the multi-enzyme
systems (1) for initial conditions (A), i.e. some constant supply of the substrate,
and (B), in which the first substrate is being consumed without any supply. The
direct adaptation of Assumption S to (1) leads to the following results:
Proposition 1. Suppose for system (1) with initial condition (A) the rate func-
tions fi (x) are Lipschitz-continuous with the constant independent of t. If for any
λ ∈ (0, 1] and x : fi (λx) = 0 ⇒ 0 ≤ λfi (x)/fi (λx) ≤ 1, the radial function of the
reachability set r(l, t) = r(l|X[t]) is the pointwise limit of rε (l, t) for any l ∈ S n
and t ∈ [0, T ], where rε (l, t) is the viscosity solution to the following equation on
S n × [0, T ] :

∂rε 1 ∂s rε ∂s rε
= Emax max fi (rε l) − − li + li+1 ,
∂t i rε ∂li ∂li+1
rε (l, 0) = ε → +0.
(here for i = 0 symbols ∂s r/∂li and li should be omitted).
As far as initial condition (B) is concerned, we will replace the coordinate x1
with x∗1 = x1 − 1. If in addition to the above we require that fi is non-negative
and non-decreasing in x1 , the following holds:
Corollary 1. Suppose for (1) the initial concentration x1 (0) = 1, xi (0) = 0 for
i = 2..n, and f0 ≡ 0. Moreover, suppose that in addition to the requirements of
Proposition 1 on fi , the fi that depend on x1 are non-negative and non-decreasing
in x1 . Then for (1) with the new coordinate x∗1 = x1 − 1 Proposition 1 holds.
The proofs of the statements above are given in the Supplement.

2.3 Examples
Here we will list the examples of (1) relevant to the enzyme kinetics, for which
Proposition 1 holds:
1. Linear mass-action kinetics fi (x ) = ki xi ;

2. Michaelis-Menten kinetics: fi (x ) = ki xi /(Ki + xi ), with substrate inhibition:
fi (x ) = ki xi /(Ki + xi + Ni x2i ), or with cross-inhibition: fi (x ) = ki xi /(Ki +
j Nij xj );
3. Power law fi (x ) = ki xci with c ∈ (0, 1);
All the above functions may be present in any combination, thereby providing
a significant flexibility for the model selection.
Moreover, the same enzyme can be used in different steps if the following
additional requirement holds: for any enzyme e used in several reactions the
value λfi (x )/fi (λx ) is independent of i for the respective i s. This will be the
case, e.g. in Michaelis-Menten kinetics since the free enzyme, and consequently,
the denominator of fi , will be the same across the respective i s. Reversible
reactions are also covered. In other cases when the star-shapedness cannot be
guaranteed, one may still use general reachable set methods [13], albeit forgoing
the advantage of the reduced dimensionality.
We will now proceed to several examples.
Example 1. The first example is a three-metabolite scheme with a constant sup-
ply of substrate zero, and it demonstrates the standard bang-bang optimal profile
[2,9,10] (Fig. 1):
ẋ1 = 1+x0 e0 − 0.1+x1 e1 ,

0.1x0 0.1x1
, t ∈ [0, 1], x0 ≡ 1, Emax = 10. (4)
ẋ2 = 0.1+x1 e1 .
0.1x1
This switching between the two regimes stems from the intuitive fact that the
rate of the reaction is increasing with the increase in x1 . As a result, the optimal
strategy is to accumulate x1 first and then to switch to production of x2 .
Example 2. The second example is a modification of the previous case with a

substrate inhibition of enzyme e1 (Fig. 2):

1+x0 e0 − 0.1+x1 +5x21 e1 ,
ẋ1 = 0.1x0 0.1x1
, t ∈ [0, 1], x0 ≡ 1, Emax = 10. (5)
ẋ2 = 0.1+x
0.1x1
1 +5x
2 e1 .
1
Now, the simple accumulation of x1 will not yield an optimal solution; due to
the inhibition, the reaction rate would decrease for large values of x1 . Hence, e1
should be switched on earlier and not to its maximal value as can be seen from
the optimal control synthesis in Fig. 2.
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Romanizers in Poland and by the Byzantine Church of Russia is a great
difficulty at the present time, but it should be understood that the Roman
Church does not dispute the validity of Byzantine orders of priesthood and
sacraments, so that the difference between Roman and Greek Christianity
does not cut so deep as that between the Roman Church and western
schismatics, such as Calvinists, Lutherans, Anglicans, and so on.
On the other hand, very important divergences have grown up in

organization between the two churches in ways which deeply affect the life
of the people. The western church, based upon the Roman Empire, has had
its waves of enthusiasm in the early Middle Ages and during the Counter-
Reformation for the unity of Europe, and the differentiation of religious
organizations within the various language groups of Western Europe has
been checked. As a result the more distant ones have seceded from Rome,
but those which remain Roman all own allegiance to the Pope, an allegiance
that creates problems for many a modern state. Reference has already been
made to the vast importance of the Jesuits in maintaining this 'universalist'
feature of religious and social life.
In the east, Constantinople, long involved in her ultimately unsuccessful

conflict with Asia and Islam, was not sufficiently strongly placed to spread
analogous waves of enthusiasm. Also her lines of communication were
decidedly difficult, and her ambassadors of religion depended more on local
factors and local aid. Then again some of the lands reached from her knew
nothing of Rome, and here her influence persisted, while others like
Hungary, &c., had been for a time in the empire ruled from Rome and
gravitated to the Roman Church. The case of Wallachia and Moldavia must
be left for discussion later on.
The Eastern Church has thus carried the universalist idea less far than the
Roman. It has developed daughter churches, sometimes with well-marked
peculiarities, within the language groups, so that now allegiance to one or
another branch of the Eastern Church is often made a criterion of nationality
in the Balkan areas of linguistic gradation and confusion. Religious
organization has tended to be within the State, and often a substitute for the
State in Eastern Europe, instead of being above the State, at least in its
claims, as in the west.
With these facts of situation, physiography, people, languages, and
religion in mind, we may now proceed to a somewhat closer survey of the
peoples in the chief natural regions of Europe east of the Teutonic and
Romance areas, allowing that the Bohemian (Czechoslovak) hill people and
the Poles have already been dealt with to a large extent.
To the north of the forest of autumn leaf-fall swamps spread far and wide
between Petrograd and Vologda, and on their northern flanks the coldness of
the soil restricts root action so much that the pines and the birch are the chief
forest trees, and the forest is only here and there worth clearing for corn
growing. This is a region for hunters and fishers and gatherers, with a few
animals and poor crops in small patches. Its peoples include a large element
related to and derived from the peoples of Arctic Asia, Samoyedes, and
Lapps, and an element among the Finns, and it is this element which has
provided the languages of the region in several parts. The Finn is a mixture
of this Asiatic-Arctic stock of broad-headed, dark-skinned people with the
tall, fair, long-headed peoples of North Europe, and as it is the former who
have provided the language, it is probable that they also provided the
women, i.e. that the Nordics were forest hunters and adventurers, moving
about without many women. In Karelia (east of the new republic of Finland)
the Finn is more Asiatic in appearance than he is in Finland itself, and for the
latter people Miss Czaplicka suggests the use of the name 'Finlanders'. In
Karelia and the river basins feeding the White Sea there is naturally also a
considerable Slavonic admixture. The antiquity of the Asiatic immigration is
a disputed point: it may be very old, as Peake once argued, but he and others
incline to make the movement fairly recent, and to connect the ancient
Arctic cultures of the region with old types of long-headed men. Near the
Baltic coast the physical type of the people becomes practically pure Nordic
in several places, and some districts on the coast speak Swedish, as do the
people of the Aland Islands.
The south-west of Finland is so much influenced by the sea that it has a

zone of the forest of leaf-fall, and thus can grow reasonable amounts of corn.
On it stand the essentially European cities of Abo and Helsingfors, and the
relation to the sea and the west is shown not only in the fact that 'Baltic' style
characterizes most Finnish things, but also in the fact that Finland became
Roman Catholic under the influence of missions from Sweden in the twelfth
century. It thus contrasts with the regions farther east, which were
Christianized by the Eastern Church. Until the rise of Russia as a power,
Swedish influence was dominant in Finland, but the growth of Petrograd and
the efforts of Russian power to organize itself in a western fashion altered
the balance and Russia became dominant, taking Finland definitely into the
Tsar's domains in 1809. In the nineteenth century long and vain attempts
were made by autocratic Russia to work in double harness with Finland,
which belonged so markedly to Western Europe by tradition, had seceded
from the Roman Church and become Protestant at the Great Schism, and
was feeling, along with Western Europe, the nationalist revival with its
literary movement attempting in this case to perpetuate Finnish and develop
it as a culture language. As in some other northern regions (notably Norway)
the aristocracy merged itself in the people, and became the leader-element in
trade and commerce. The small amount of good land has made it a precious
possession, and the Finlanders are keenly interested in peasant
proprietorship. In all these ways the contrast between them and Russia is
strongly marked, and the new rulers of Russia have evidently recognized this
in their treaty with the now sovereign state of Finland. Finland's timber is a
precious asset, and her cattle are likely to bring her some wealth; her future
is as a Baltic people, and it may be hoped a member of a future Baltic
federation. The Alanders inhabit a maze of islands, which are a partially
submerged extension of the Finnish plateau; their historic associations have
been with Finland, but, like the people of some coastal regions of Finland,
they speak Swedish. The League of Nations has suggested for them a
scheme of local autonomy under Finland, and this is under consideration, but
they seem to wish for a closer link with Sweden. Such a link educationally
and religiously would be of value, and we have here merely one more
example of the hampering effects of our present undue insistence on the idea
of the sovereign state rather than on that of the United States of Europe. The
Karelians and other Finnish peoples of the north, east of Finland, have been
affected a good deal by monastic settlements made by the Eastern Church;
they may get a living partly by lumbering and partly in fur trade; cultivation
and even stock-raising must remain poorly developed.
Turning south of the line from Petrograd to Vologda we are, at least

theoretically, in the zone of the forest of leaf-fall, that is a forest with the oak
and birch, not, however, the beech. Here again the Baltic coast lands have
peoples strongly marked off by culture associations from those of the
interior, but, as regards the interior, the penetration of Finnish or more
broadly Asiatic influences is not nearly so marked until we come to the
Volga below Kazan, where are to be found the Mordva. In this eastern region
are also found groups of Tatar speech and Asiatic origin, some of whom
were gradually forced by past Russian governments to give up nomad
pasturing and become settled cultivators. A Tatar republic now centres round
Kazan (1921). An Asiatic influence may nevertheless be traced far and wide
in the physique of the Russian people of Muscovy, though they owe their
main inheritance to the broad-headed, dark, central European stock which
has colonized the Russian forest bit by bit from the more open lands of the
Polish-Galician platform, moving around the south side of the Pripet
Marshes and entering the Muscovite forest via the Dnieper crossing at Kief.
An important element in the life of the people has been their association with
the mediaeval fur trade of the Hanse, and a study of Russian physique
suggests a Nordic sprinkling all over the country, and especially among the
landowners; but the villagers are mainly of the broad-headed type,
characteristic of the mountain axis of Europe, albeit in the better lands taller
than they are in the Alps and Cevennes, and in other ways also more like
some types found in the Balkan Peninsula.
The social study of the people of Central Russia is probably one of the
best clues to the understanding of that stage of our own past, in Western
Europe, when settlement in forest-clearings was the most marked feature of
development of social organization. The Tsar's Government had in recent
years persisted in a policy of modernization of rural arrangements, but, in the
words of a supporter of that policy, the villagers fell back upon their old
communist schemes as soon as the war crisis made them rely on themselves;
it was the one scheme they understood.
How far this is really true, or how far some at least of the villagers tried
to develop individual proprietorship, must remain doubtful, but there can be
no doubt that localism and the Soviet idea have become marked features in
Russia, with the paralysing of the more modern schemes of life which were
previously trying to spread in the country with the growth of industry and
commerce. That the more modern schemes seemed to permit a larger
population seems clear, but that they were faced with difficulties due both to
climate and to history is not always appreciated. The west in the nineteenth
century was too apt to think its individualism applicable to all conditions and
peoples the world over; it had not sufficiently understood its individualism
as a historic growth under western conditions which masked the conflict, for
example, between it and the Christianity the west supposed itself to accept.
Of the life of the Russian village we shall have more to say later on, but it is
well to have its attitude in mind so that we may contrast this with the
characteristics of the Baltic fringe. Here, since the war, new states have been
created and recognized (1921) by the League of Nations under the names of
Esthonia, Latvia, and Lithuania.
The two first have a Baltic-German element which has in the past been a
land-holding class, and has its historic links both with the Teutonic Knights
and with the Hanse—for Riga is an old Hanse city of special importance.
The Finnish element is strong enough in Esthonia to impose its language

on the people, but farther south tongues of ancient Baltic lineage are
dominant, and the new states are largely on a basis of peasant language, the
German elements being disregarded, and to a considerable extent
dispossessed. Having passed through a stage of feudal subjection, the
peasants are bent on individual proprietorship, as they were in the eighteenth
century in France; and the war has brought a social revolution along this
border zone between the domains of the two churches, with some marked
resemblances to that of 1789-93 in France. In Esth-speaking country there is
but little forest that is not pine, and only 10 per cent. of the soil can be made
arable, it is said. Though the Lett country is better, it can grow neither beech
nor oak to any extent; it is interested in dairying, and in this matter naturally
has commercial links with Denmark. The Lithuanians are a grave European
problem; they escaped the Germanizing efforts of the Teutonic Knights, and
felt instead the Polonizing of their aristocracy, the abler scions of which have
long found opportunities at Warsaw. Set in the Lithuanian country is Vilna,
the station on the one reasonably dry entry from the west into Central
Russia, and therefore a trading town with large German, Jewish, and Polish
elements illustrating more tragically than any other town the difficulty of
creation of states in this eastern boundary zone of Western Europe. The
forests of Lithuania are very important for the country's economic future.
Thus south, as north, of the Petrograd-Vologda line, we have contrasted

conditions in the west, the centre, the east, but on the south the Finn element
is much less marked, and the central European one much more so. Moving
south again beyond the Pripet marshes we find corresponding contrasts.
On the west the Polish platform grades south-eastward into the Ukraine
or Border Land, with its great stretches of loess, but also its patches of
forest, especially near the waterways. The forest thins out towards the open
steppe of South Russia, which in turn grades into desert patches near the
Caspian. The open steppe of South Russia is but the continuation of the great
steppes of Asia.
To understand the peoples of this belt let us remember first that the
ancient graves contain many long-headed skulls, and that this element in the
people probably persists to a greater extent than average figures show, in
spite of the pressure of central European, of late at least Slavonic-speaking,
immigrants from the west via Kief, and of Tatar immigrants from the east.
Byzantine elements from the south need also to be allowed for in the people
as well as in their civilization, in which matter Kief has become as markedly
the Byzantine sacred city of Russia as Canterbury is the Romano-Gallic
sacred city of England.
In the Ukraine Poles have done a good deal of organizing work, and put
themselves in the position of landowners and leaders over a Ruthenian
peasantry. The landlords were attached to the Roman Catholic faith, but the
peasants to the Uniate Church until the latter was crushed by Russia. The
border of the Ukraine towards the steppe is a very doubtful matter. Here is
the zone of unrest, with Tatar pressure at times and European pressure at
others; it is the limit of the settled life, and the cultivated patches have
needed specially watchful defence. Under these conditions the Cossack
people have grown up with a military order of society and landholding for
service. The people seem to include an element of the old long-headed
population (see pp. 11, 14, and 77), together with both Slav and Tatar
contributions, Jews and Germans in the towns which are mostly of recent
creation, and a motley gathering of escaped serfs and landless men from all
around.
The Don Cossacks are fairly distinct from the Orenburg and Siberian
Cossacks who live east of the desert patches that lie north-west of the
Caspian Sea. In what is broadly Cossack country lies the very different
Kuban country, with an almost Mediterranean climate and possibilities of
fruit cultivation; it is said to have had an autonomous organization of its own
for some time during the recent years of unrest. Its people are doubtless
related to various elements among the Cossacks, but one gathers that the
descendants of old traders are more marked than elsewhere. The Tatar
(Turki) groups are so obviously an intrusion from Asia that we need not say
much about them as such; we may more profitably think of them as pressing
upon Europe at one time and being pressed upon by Europe at another.
Their tribal organization on a kinship basis and their mobility have given
them a power and a cohesion for offensive purposes from time to time, and
as Huns, Magyars, Bulgars, Szeklers, and Tatars, they have been formidable
hindrances to the settlement of East and South-east Europe on western lines.
We may note first that Huns, Magyars, Szeklers, and Bulgars, penetrating far
from the South Russian steppe either past the Iron Gates, or through the
Carpathians or over the Danube into the Balkan Mountains, have become
settled folk.
In Hungary they have formed a landed aristocracy with its rural

dependants, while leaving the peopling of the towns largely to Jews and
Germans and persons of mixed blood. In the Balkan Mountains under less
spacious conditions and with Turk interference they have merged into a
South Slav people, but have modified that people and its language in the
course of the process. In South and East Russia there are many groups still
distinct, and the Crimea has long been theirs in principle. The relation of
these Asiatic warriors with Muscovy makes up the political history of the
Middle Ages in the future Russian plain, and when that plain did become
Russian, its religious autocracy found greater possibilities of co-operation
with the Asiatic element than with the Western Powers then developing so
fast towards industrialism. So it came about that Peter the Great's historic
experiment in westernization, difficult for reasons of climate, position, and
opportunities, failed, and the Tsardom was drawn towards the Orient on the
whole against its will.
The westward path of the Asiatic herdsmen beyond South Russia led
them into Moldavia and Wallachia, where the native Vlach population
sought refuge in the Carpathians and in the hills of the centre of the Balkan
Peninsula. It is a population with a language of Latin syntactical affinities,
and a 60 per cent. Slav vocabulary, and is spoken by people who looked
back with pride to the days of Roman occupation of their land as Dacia. So
the Vlach people, essentially Central European round-heads like the Slavs
generally, have come to be distinct from their neighbours in speech and in
pride. In the matter of religion the openness of the Danube entry and the
coastal ways up the west side of the Black Sea have made the people
members of the Eastern Church so far as Moldavia and Wallachia are
concerned, but the Vlachs of the Transylvanian hills are, or were, to a large
extent members of the Uniate Church (p. 70), intermediate, as has been said,
between the Roman and the Eastern. After centuries of subjection and
fractionization the Vlach peoples have (1919) suddenly found themselves
united in the new Rumania, with the political and agrarian influence wrested
from their former Magyar, Szekler, and German lords, and the peasantry of
Wallachia and Moldavia have also secured a good deal of the land
previously in aristocratic, though in this case often not alien hands. The old
direction of the country was in the hands of the aristocracy, and was often
much criticized in the west. The Jewish and German town populations were
said to be specially held down. Whether the new government will merely
continue the old with a peasant admixture or whether it will seek to take a
new line, remains to be seen. It is at any rate interesting that this large
language group is, for the first time, a governmental unit, and tragic that so
inexperienced a group has within it such large and, for that matter, valuable
elements of alien language. It is said that the Oriental aspect of society is
well marked in the lesser towns, the greater having been westernized, but it
is questionable whether we should not be more correct in describing these
lesser towns as more resembling our own in early mediaeval times before the
garden-closes were built upon to accommodate people crowding within their
walls for protection.
The Vlachs beyond the new Rumania, in the centre of the Balkan
Peninsula, illustrate for us a noteworthy problem of that troubled region.
Whereas if we wish to get a picture of the early stages of the settled life of
cultivation in Europe we naturally look to Russia, we may go to the Balkans
for glimpses of the remnants of the still earlier scheme of society when
kinship groups moved from place to place with flocks and herds. In the
Peninsula the western mountains shelter many a clan of ancient local
lineage, and much as these mountain clans have been affected by Slav,
Bulgar, Greek, Roman, Turkish, Magyar, and German-Austrian pressure, a
considerable group have remained true to their pre-Slavonic language
(Albanian), and, despite deep religious differences amongst themselves,
seem to tend towards some vague national unity, largely as a protection
against Greek and Slav in the next generation. It is well to realize that these
old populations, even when Slavonized, are often most distinct from the
Slavs, and that they and the Vlachs are the nearest approaches we have to an
autochthonous population in the Peninsula. They for the most part limit their
movements to seasonal shifts up and down hill, and, like the Highlanders of
Scotland and others similarly situated, have done their share of raiding on
valley cultivators, for if 'the mountain sheep are sweeter, the valley sheep are
fatter', as Peacock put it. Among the Albanian peoples the Greek Church has
done a good deal of propaganda at various times, and as they are near the
Adriatic and the Roman Via Egnatia, the Roman Church has also used
opportunities of reinforcing them against Greek pressure. Moreover, all
along this mountain country Manichaean ideas replaced old heathendom and
primitive Christianity alike, and with the Manichaean objection to
symbolism and all approach to idolatry there was a natural tendency to
accept Islam without too much difficulty, when it was brought by
conquerors. So along the western mountains of the Balkan Peninsula are
many old groups confirmed in their ancient possessions by the Turk, and
practising Islam in succession to Manichaean doctrines rather than to
Christianity. As the people on the fringes of the truly Albanian clans speak
two languages, in many cases there is as much doubt about the proper
political boundary of an Albanian state as there would be about that of a
Welsh state were it proposed to make one separate from and hostile to
England! Much harm has recently been done by conscientious demarcators
taking the frontier line along 'empty' ridges which were really summer
pastures or ways thereto for many a shepherd clan now cut off from its
livelihood and ruined or forced to maraud. Among the Albanian clansmen
the leaders are often rather fine types with the strength arising from a long
maintenance of tradition, the change to Islam not having been as
fundamental as might be supposed. It is the more regrettable that the
antipathies between them and their Slavonized brethren should have become
so acute.
In the west of the peninsula, north of the region of Albanian speech,

many of the people are Slavonized autochthones, rather than real Slav
intruders, and this is true of the mountains of Montenegro and of Bosnia, in
the latter of which large numbers of the landed folk are Muslim. The Slav
peoples have, however, penetrated everywhere from the valleys of the Save
and Morava, though one can still often recognize the old hill-type at sight.
Both are broad-headed, and are branches of the same basal stock, but the old
hill-type is often bigger and more lithe, and there seem to be accompanying
mental differences. At any rate these distinctions were found practically
useful in contacts with refugees from Serbia in the recent war. The
distinction between the Illyrio-Slav and the Bulgar-Slav on the west and east
of the Balkan Peninsula is one with indefinite gradations and with collateral
complications due to Vlach elements on the hills and long-established Greek
elements along the coastal plain. The appeal to race and language as a basis
for political division is almost futile; the appeal to history is misleading, for
as in the early west of Europe, so also here we find sudden growths and
more sudden collapses of empires based upon the ability and ambitions of a
leader; the appeal to religion has been encouraged by the fact that Eastern
Christianity tends to encourage national churches and has education in its
hands. We thus find that the Bulgars by educational propaganda made their
variant of Balkan speech the definitive one in most of Macedonia, and that
the conflict between them and the Serbs has become fatally acute, the more
so as both have been used as cat's-paws by the Great Powers of Europe ever
since the Turkish hold weakened. The erection of organized political
frontiers within the Peninsula limited the power of movement of the
wandering shepherds, and seems to have affected especially the Vlach
elements of the centre, which are said to be losing their separate character
and to be settling down. It also sharpened the internecine conflict, especially
since Russia, France, and Britain saw their opportunity of using Serbia, from
1906 onwards, to resist the Central Powers, while Bulgaria became of less
interest to the Tsardom as she grew strong enough to do without Russian
tutelage.
Broadly then, while Russia gave us an example of the poor success of an

attempt to fasten a State organization on a population deeply immersed in
localism and traditionalism but settled and cultivating the land, the Balkan
Peninsula illustrates tragically the weaknesses of competing attempts to
fasten State organizations on a population, parts of which have as yet barely
reached the stage of settlement. The difficulties within the Peninsula are
undoubtedly enhanced by the sharp contrasts between the highland interior
and the coastal fringe on which for milleniums already the influences of
Crete and Babylon, Phoenicia, Greece and Rome have been playing.
It is a Mediterranean fringe with its hoe cultivation and olive-trees
already long established as the successors of an ancient barley culture, and it
has trade as such a long-standing secondary feature of its life that observers
not infrequently mistake it for the primary one. Roman ideas have spread
along the Istrian and Dalmatian shores, and, in spite of Slavonizing
influences, have remained strong at Zara, Fiume, and Trieste, while, though
Croatia and Slavonia have remained Slavonic, their religion has become
Roman Catholic and their alphabet western. It thus comes about that a not
very deep difference of language between the Slav regions of Serbia, on the
one hand, and of Slavonia and Croatia on the other is emphasized because
the one uses the Cyrillic alphabet, the others the western, and each has its
systems of schools on a religious basis, a serious problem for the new State
of Yugoslavia. It is probable that the recent settlement of the Adriatic quarrel
between Italy and Yugoslavia represents a fair compromise so far as the two
are concerned.
South of Albania and around the Aegean the coastal fringe is dominated
by the Greek element, and the new Greece claims to include all these coastal
lands and to have the reversion of Constantinople, the great inter-continental
city which at the same time commands the way from the steppe-lands to the
Great Sea. Constantinople is the more maritime successor of the less
maritime Troy of antiquity, and this, in conjunction with its history as the
basis of the Eastern Empire, the head-quarters of the Eastern Church, and the
seat of the Caliphate of Islam, all seems to argue against its absorption in a
nation-state organization and its government by trustees acting not less for
Islam than for Europe. The problem of Constantinople is also that of the
coastal fringe, wherever the interior is non-Greek. On the language basis the
Greek claim is strong; on the economic basis, again, the traders have rights
of protection, but the cutting off of the coast from the interior must be
prejudicial to the latter. Unfortunately, a trusteeship for government is almost
put out of the question by the fact that practically every European Great
Power has intrigued for a paramount influence, and all are justly suspect.
Thus both the national and the international solution of the problem of a
political and social organization of Balkan life seem fraught with difficulty,
and one can but urge the old, old argument against preaching 'Peace, peace',
where there is no peace. The present hope would seem to be in the smaller
nations of Europe and perhaps in the American powers, for Latin America
seems likely to wish to play such a part in the reorganization of the world as
its growing economic importance justifies.
The real difficulties of the Balkan peoples are enhanced in every way by
their disastrous political history, for none have, for centuries past, had
reasonable opportunities of self-expression. They therefore lack the
experience and the discipline of government, and they have little effective
written tradition, with the result that what is written now is often very
different from the spoken language of the peasantry, and is correspondingly
artificial and lacking in healthy standardization. One may contrast the good
fortune of the Norwegians in having relatively peaceful opportunities of
revival of folk life and in having the wise and luminous Bjornsen to develop
literary expression in continuity with folk tradition.
Of the Turk in Europe one cannot at present say much that is definite. He
is largely Europeanized in physique, and it is doubtful whether much that is
truly Turk remains in Europe outside eastern Thrace. The Muslim elements
in Albania and Bosnia have other origins for the most part, as has been
discussed. Constantinople and Adrianople are markedly Turk.
While, then, the various new states of the Peninsula are largely on a
language basis, it should be noticed that Vlach-speaking peoples are
scattered in groups in what is now Yugoslavia, and their numbers are
variously estimated up to 250,000 or more. A considerable portion of
Yugoslav Macedonia would probably consider itself Bulgar, and there are
Greek elements in the Macedonian towns. Apart from Greek elements in the
towns there is little that is alien in the reduced Bulgaria. Rumania has groups
of many languages and traditions in all her newly acquired territories, and
will need to exercise every care to prevent serious trouble in the near future.
Yugoslavia includes a good deal of German, a little Italian, some Magyar,
and some Rumanian, as well as Greek and more or less Bulgar elements, and
a neutral commission should go carefully into the question of the Albanian
boundaries. Italy's gains in Istria include a large Yugoslav element. Greek
acquisitions have such a mixed population that little can be stated in detail.
Finally, the Jewish element is of widespread importance in the towns; the
Ashkenazim (Central European) element being very strong in Wallachia, and
especially in Moldavia, and the Sephardim element (once Spanish) having
its head-quarters at Salonica. Before leaving the Balkan peoples it should be
pointed out that, apart from their ancient hatreds, there is really every reason
for mutual help between them. Rumania with its wheat and maize, Serbia
with its forest-fed pigs and its plums and other fruits, Bulgaria with its mixed
farming, and the Greek zones with their oil and wine, could supplement each
other if suspicions were diminished and mutual credit arranged. The Greek
element, with its long experience of commerce, would be a natural
intermediary, as Venizelos saw when he planned a Balkan Federation; the
obvious danger would be that of exploitation of producers by middlemen,
especially if the latter were in a strong position politically.
The use of Czech, Slovak, Polish, Ruthenian, Serb, Croat, and Slovene
for centuries largely as rural languages, with German to a considerable
extent a lingua franca for educated intercourse, and Magyar imposed in and
around Hungary by an aristocracy, hindered the growth of the Slavonic
languages until the nineteenth century, and in that century it has been
especially Czech, Polish, and Croat that have pushed forward towards the
status of languages of civilization. Ruthenian remains in a sense the most
backward member of the group, so much so that its claims have been
conspicuously disregarded by the makers of the recent treaties. The
Ruthenes west of the Carpathians inhabit a poor region which is to be
included in Czechoslovakia with a measure of local autonomy. Ruthenes in
what was once Galicia are largely under Polish proprietors, and that territory
is to be incorporated with Poland, while the Ruthenes of the Bukovina and
the west bank of the Dniester are now included in the enormously enlarged
Rumania. It may be that under the new conditions these peoples will settle
into the framework created by the treaties, a framework based to a
considerable extent upon physical geography. But, on the other hand, if the
Ukraine should become strong and the Ruthenian language develop, there is
undoubtedly the possibility of the growth of an idea of 'Ruthenia Irredenta'
which may bring difficulties later on. At present Ruthenes might well use
Russian as their language.
This seems the most appropriate place for a brief catalogue of the peoples
of East-Central and Eastern Europe whose languages do not belong to the
Indo-European family, though many have already been mentioned. The
Lapps moving between the high moorlands of Scandinavia and the Kola
peninsula speak a language belonging to the Arctic-Asiatic group and are
nomad herdsmen of the reindeer; their numbers are small, but they provide a
curious background to Scandinavian life; and a certain amount of
intermarriage has caused some Swedes to carry their features. Forms of
Finnish speech, all more or less akin, are widespread from Finland to the
Urals, and the nationalist and democratic movements of the last century have
strengthened the speech of the Finlanders proper at the expense of Swedish,
the old language of external culture relations in West Finland, and of Russian
which the Tsarist government sought to impose. Esth is closely related to
Finnish, and under the new conditions of nominal independence may
maintain itself by association with Finnish in spite of poverty of land and
people. Livonian is related to Esth and still survives in parts of Latvia.
Various groups of Finns, retaining their languages, still remain distinct in the
government of Perm and near Kazan and Saratov. The Tatar groups on the
grassland and desert-border in South-east Russia so obviously belong to Asia
that they may be omitted from this survey. Like so many mountain regions
the Caucasus forms a refuge for ancient racial types, old customs, and old
forms of speech, but a survey of these would take us far from European
problems.
Bulgar has been mentioned as a language with a Tatar element, though it

has been very largely Slavonized, but this fate has not overcome the Magyar
tongue, which is the distinctive feature of the erstwhile ruling caste in
Hungary and Transylvania. The language is used both by the Magyars of
Hungary and by the Szeklers, who are a people of closely related origins, in
parts of Transylvania. The people are almost completely Europeanized in
their physique, but as they secured some degree of national cohesion and of
close attachment to their soil at an early stage of history, their language has
lived on, and of late its use has been fostered by political ambition; it has
become a mark of a ruling caste. It may now become the rallying ground of
aspirations for national recovery after the collapse of 1918 and the severities
of the recent treaty. The Powers of Europe in framing the new boundaries
have at least suggested a campaign of linguistic nationalism to the Magyars,
for the reduced Hungary has considerable numbers of people speaking its
language who are now subjects of the states around its borders. There has
been no incentive to outsiders to learn Magyar, and it remains isolated in
Europe, useless beyond its homeland and unlikely to contribute much to
other languages.
9
Some Phases of Evolution of European Life before the

Industrial Revolution
We have now glanced around all the chief language groups in Europe,
and in the course of this rapid survey have noted that whereas the peoples of
Romance and Teutonic speech have built up the organization known as the
nation-state, in most cases on a basis of linguistic unity, the peoples of the
Slavonic regions, with the partial exception of Bohemia, have hardly
achieved this. The intermingling of peoples and the difference of tradition
between town and country over wide areas are in part the cause of this, but it
has also been suggested that, in the east of Europe, we have still surviving an
earlier stage of the process of settlement in the cleared forest than farther
west, while in the south-east we note the persistence of elements still hardly
settled at all. It will therefore repay us if we now try to make a rapid survey
of the evolution of the process of settlement with its variants in different
regions and of the indications of persistence of different stages of the general
process in various parts, chiefly of Eastern Europe.
All the evidence we have goes to show that after the Würm Ice Age the
first European peoples were hunters apparently spreading up from the
western Mediterranean basin. To them must be added the hunters who seem
to have spread along the loess westwards. These two groups were bearers of
the Aurignacian and Solutrean cultures of anthropologists. Hunting has
remained a feature of European life ever since, but time has brought too
many changes in the hunter's life and position to make it profitable to discuss
possibilities of social survivals from so long ago. The partial regrowth of the
glaciers (Bühl period) modified the hunting life; and associated with this
cold-cycle civilization (Magdalenian Age of the anthropologists) was the
great development of pictorial and sculptural art which has so astonished the
world since its rediscovery. As the cold passed away, this time definitively,
the sinking of the west converted Britain and Ireland into islands, and so
brought maritime influences far into the Continent, with the result that
forests spread far and wide with wolf, bear, boar, wild cats, and birds of prey
to dispute them for a time with man. The zone of loess and some wind-swept
or calcareous areas near the sea or on the hills remained relatively clear of
forests and dry enough for occupation by man, and on these areas men
practised the art of herding animals, moving from pasture to pasture, as
circumstances required or, increasingly, with the cycle of the seasons. There
were possibly already cultivators beginning to grow barley as a supplement
to herding or hunting. We should, however, be careful not to argue that the
beginning of cultivation necessarily implies settling down in one place; the
Vlachs often sow and reap a barley crop without making more than a very
temporary sojourn.
The development of civilization was not purely and simply a

development of herding from hunting, nor was the herding purely analogous
in social features to that of the tribe on the grasslands. The development was
accompanied by differentiation, and it seems clear that herding was very
early carried on with much greater restriction of movement than on the
grass-lands and desert borders of Asia. There was quite early a tendency to a
regular cycle of seasonal change (transhumance) rather than to broad
wandering, and our territorial instinct is very old.
With this statement properly goes another to the effect that some kind of
cultivation became a supplement to the herder's life almost at the outset, and
we may further surmise that some part of the population would soon remain
near the more cultivable lands to guard them. Thus restriction of seasonal
wandering to a part of the population is another very old feature of life, one
judges, in many, though not in all parts of Europe. In the Val d'Anniviers, so
clearly marked that territorial disputes could hardly arise, and at the same
time freed from ravages of wild beasts, practically the whole population still
moves up and down with the change of the seasons, though it has permanent
buildings at each of its four stations. Reference has already been made to the
Vlach wanderers of the Balkan Peninsula, and one might also speak of the
Lapps, whose movements along the moorlands of Scandinavia were
formerly a source of frontier trouble between Sweden and Norway.
With the development of the phase of civilization called Neolithic in
Europe goes the making of pottery, which implies tendencies to live in one
place at least for a time, the utilizing of particular types of stone from
particular spots suggesting a long-continued exploitation of the special
source, the making of very definite settlements on the Swiss lakes, and the
developing of crop-growing and weaving and so on by their inhabitants.
Both settlement and trade seem indicated, but it is most probable that many
of the lake-dwellers also used the spring pastures on the hills. The
distribution of the great stone monuments and several other matters indicate
the growth of long-distance sea trade about the end of the Neolithic Age and
in the period when the use of copper and bronze was spreading round the
coasts of Europe; and a recently discovered Mesopotamian tablet dated 2800
B.C. gives facts about tribute paid to Babylon from tin lands beyond the
Great Sea (Spain). Development of settlement must have continued in the
Bronze Age, still mainly on the naturally open lands rather than in the
cleared forest, and it is a notable fact that, save in a very few areas with
special explanations available, the regions of megaliths do not show
examples of the kind of village, with strips once owned in common, which is
so characteristic of regions of cleared forest, though not the only type there.
The hardening of bronze was one of the most important facts affecting
man's advance in the Bronze Age, and we have abundant indications (see
papers in archaeological and anthropological journals by H. J. E. Peake) of
man's ability to attack the forest seriously ere bronze gave place to iron. The
attack on the forest was undoubtedly redoubled when man acquired iron
weapons, and so the Early Iron Age witnessed extensive settlement in forest
clearings in Europe north of the Alps, and with that went increase of corn-
growing. South of the Alps the warming of the climate after the Ice Age had
helped to reduce the forest, especially in view of the large stretches of
limestone and the sharp slopes which have always hindered regrowth of
forest once destroyed.
The Mediterranean region, by reason of the long summer drought, has

become with the establishment of its present climate less fit for pasturing of
animals and more suited to the goat than to cattle or sheep. As a result of this
the destructive goat has reduced the forests and hindered their regrowth. The
difficulty of stock-raising encouraged efforts towards cultivation, which is
certainly very old in the Mediterranean region, and has passed through
several phases that need elucidation. It seems probable that barley
cultivation was established very early, and bee and fruit culture were
gradually gathered around it, the olive proving invaluable as a substitute for
animal fat. But ere the olive could be grown in quantity there had to be a
good deal of organization, for it does not begin to bear till it is almost eight
years old, and is in full bearing when it is nearing its thirtieth year. To wait
for the olive, therefore, meant possession of some reserves and assurance of
food supplies, such as imported grain, ere much land could be turned into
olive groves. War and unsettlement worked against olive culture, for the
risks of destruction of an olive grove were then serious, and the
consequences disastrous.
If, however, olive culture was, on the one hand, the result of a measure of
peace and prosperity, it was also in most cases the presage of further growth
of prosperity; the harvest was reasonably assured and immensely valuable,
especially as it could be transported far and wide by sea. The relation of
olive culture to the classical period in Greece is well known. We seem to
have grounds for associating city growth in the Mediterranean with trade and
the spread of large-scale olive culture as well as with the question of
defence.
Both north and south of the Alps the dependence of man on cereals after
he gave up his milk and flesh diet seems to have made him desire salt, and
the Early Iron Age settlements of Gaul are closely related to sources of salt,
while the Mediterranean coast-lands had ample opportunities of salt getting.
The pig had been domesticated by this time, and the salting of bacon and
fish gave a reserve for the winter, but it has been claimed that salt was also
in request for forms of porridge, &c. In thinking of the early settlements we
should remember that north of the Alps there was perpetual danger lurking
in the dark forest, while in the south there were the rough goatherds of the
mountains.
In the last millennium before Christ the worsening of the Scandinavian

climate drove peoples southwards towards Gaul, and thus led to a growth of
hill-fortress towns, of which the supreme examples were Alesia, Gergovia,
and Bibracte, and from Gaul the building of these fortress towns spread, with
sea commerce, up the west coast of Britain, where Tre'r Ceiri on Yr Eifl in
Carnarvonshire furnishes us with one of the best examples of this type of
settlement of the Iron Age or Romano-British times.
For the purposes of this sketch it is not necessary to go into great detail
about the Roman efforts, but we should note that within the bounds of their
Empire they spread wheat cultivation, road communications, and their legal
system, and that along with this seems to have gone a cheapening of iron.
All these changes helped to knit the people to the soil, to make
neighbourhood take the place of kinship as a basis of association, to root a
language in the people's hearts. It is the men who 'lacte et carne vivunt', as
Caesar puts it, who organize on a kinship basis, move from place to place,
and lack the written records which do so much for language fixation.
We thus see in Gaul villages of various types in regions of differing

history and opportunity, but pre-Roman fortress towns and Roman cities
between them networking the country and related to roads built or adapted
by the conquering engineers, and we note the implanting of linguistic
features that not all the shocks of later disruptions have contrived to uproot.
In Britain again are villages of varying types, pre-Roman or Romano-British
fortress towns, chiefly on the west coast headlands, Roman cities for the
most part speedily ruined, and Roman roads. The difference in the vitality of
the cities is to be correlated with the difference as to language; the Roman
elements in our language are for the most part the result of reintroduction
later on. The Roman element in Welsh is usually allowed to be important.
If the spread of the rural Franks and of the Anglo-Saxons into the
erstwhile Roman domains led to the submergence of the old cities and to
much village foundation, there is at any rate a growing opinion that it did not
destroy all continuity in either Gaul or Britain, that a good deal in our rural
life goes back, as above hinted, to the late Bronze Age. The system of the
manor under which the villagers give service to a military protector is too
easily mixed up with the village system in discussions. The manor, with
complex origins, is characteristic of post-Roman days of movement and
strife. The civilizing element promoting agriculture and the law is furnished
by the Church, which, with the centuries, spread its work over the Rhine,
beyond the bounds of the Empire, right away to the limits of Europe-of-the-
Sea, that is of the lands near Baltic or Mediterranean, or west of a north-
south line near the east ends of those seas.
With the settling down which heralded the Middle Ages after the Dark
Centuries of movement and war, we thus find the following broad facts. In
the Mediterranean, where fruit culture and the city-state and trade were
already old, that type of life reasserted itself even though the division of life
on the north and the south sides (characteristic long before in Phoenician
times) of the sea made grave difficulties.
In Spain the conflict between Islam and Christians inhibited the

development of both and delayed everything. In both cases the military
organization was unhealthily important, and the Muslim of the south kept
much of their old social scheme based on the tribe, whereas they should have
been adapting themselves to the rich land of Andalusia which they held. The
result of the inhibitions made the Muslim far more of a misfit in the
Andalusian garden than were the Christians on the heights of northern Spain,
where seasonal movement of flocks and herds (transhumance) is still very
important. The Muslim of the south thus gradually declined both in value
and in influence, and though in earlier times they had been far more cultured
than their Christian foemen, they had dropped far behind in organization
before their subjugation in the fifteenth century. One should nevertheless
bear in mind possible valuable survivals from the Muslim in matters of detail
or of individual work. In Gaul cultivation had spread and had improved
under monastic leadership; markets were growing under protection of the
cathedrals, and were becoming the town centres that have persisted as the
highly characteristic market towns of the Paris basin. After years of rivalry
with Frankish dialects the old Roman heritage of language triumphed with
some compromises, and became the langue d'oïl, the speech of the Paris
basin and upper Burgundy, and the progenitor of standard modern French. In
Britain the rural element seems to have predominated until Gaulish
influences again became strong in the eleventh century.
In the lands beyond the Rhine the abbeys were promoting agriculture,
with towns growing some time after the corresponding phases were carried
through in Gaul, and with the power of the war lord very strongly marked. In
the Slavonic lands the phases of settlement and town growth are later still
with the church and the war lord in close association, as is exemplified both
by the Teutonic Knights in East Prussia and by the inclusion of the cathedral
in the castle precincts in Prague and Cracow.

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Full download test bank at ebook textbookfull.

11th International Conference on

Practical Applications of Computational Biology and

8th International Conference on Practical Applications

Practical Applications of Computational Biology &

Advances in Bioinformatics and Computational Biology

GeNeDis 2018 Computational Biology and Bioinformatics

Introduction to Bioinformatics with R A Practical Guide

Complex Networks amp Their Applications VI Proceedings

Proceedings of the International Conference on

More information about this series at http://www.springer.com/series/11156

Juan F. De Paz Tiago Pinto

11th International Conference

Mohd Saberi Mohamad Tiago Pinto

ISSN 2194-5357 ISSN 2194-5365 (electronic)

© Springer International Publishing AG 2017

Printed on acid-free paper

This Springer imprint is published by Springer Nature

Biological and biomedical researches are increasingly driven by experimental

Mohd Saberi Mohamad

Mohd Saberi Mohamad Universiti Teknologi Malaysia

Alejandro F. Villaverde IIM-CSIC, Spain

David Hoksza Charles University in Prague,

Nuno F. Azevedo University of Porto, Portugal

Diogo Martinho Polytechnic of Porto, Portugal

PACBB 2016 Sponsors

S2P: A Desktop Application for Fast and Easy Processing

Classiﬁcation of Colorectal Cancer Using Clustering and Feature

Towards Trustworthy Predictions of Conversion from Mild Cognitive

A Critical Evaluation of Automatic Atom Mapping Algorithms

Hugo López-Fernández1,2,3 ✉ , Jose E. Araújo3, Daniel Glez-Peña1,2,

Miguel Reboiro-Jato , Florentino Fdez-Riverola1,2, and José L. Capelo-Martínez3

Abstract. 2D-gel electrophoresis is widely used in combination with MALDI-

Keywords: Protein identiﬁcation · Data processing · Bioinformatics tools · Open

© Springer International Publishing AG 2017

The scientiﬁc community is particularly interested in the challenging task of ﬁnding

2 Materials and Methods

2.1 Case Study

As a case study, a dataset composed by 14 patients plus 1 healthy group of 6 individuals

3 Results and Discussion

needed to reproduce the steps explained below is available at http://www.sing-

Fig. 1. Schematic S2P ﬂow diagram.

Fig. 2. Screenshot of the S2P integrated analysis window.

Fig. 3. Heat maps showing the diﬀerentially expressed spots.

Fig. 4. Box plots of the diﬀerentially expressed spots.

S2P (http://www.sing-group.org/s2p/) is freely distributed under license GPLv3,

Stanislav Mazurenko1(B) , Jiri Damborsky1,2 , and Zbynek Prokop1,2

Abstract. This article studies the time evolution of multi-enzyme path-

Keywords: Enzyme kinetics, Optimal control, Synthetic biology,

1.2 Mathematical Setup

describes limited resources of a cell that force it to choose which enzyme to

1.3 Optimal Control

computationally intensive than the maximum principle, it provides the time-

2 Star-Shaped Reachable Sets

2.1 Reachable Sets and Optimization

that is the viscosity solution to the following partial diﬀerential equation on an

where ρ(l |F ) = sup{ i li yi |y ∈ F } is the support function. This result, together

2.2 Star-Shaped Sets Generated by Multi-Enzyme Pathway

The proofs of the statements above are given in the Supplement.