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PRINTED: Bioinformatics and Computational Biology Books
Lawrence Hunter (editor), Artificial Intelligence and Molecular Biology
This book is intended for computer scientists and mathematicians who are interested in an introduction to molecular biology and the applications of artificial intelligence to molecular biology. It is now out-of-print, and is being distributed for free on the web.

Andy Baxevanis and Francis Ouellette, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins John Wiley and Sons, 1998; 2nd edition April 2001
"- provides a broad overview of the basic tools for sequence analysis - For biologists approaching this subject for the first time, it will be a very useful handbook to keep on the shelf after the first reading, close to the computer." -Nature Structural Biology
"- should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data." -Science
"- a useful resource to help biologists extract the maximum value from their data." -Cell
" - a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis - The accomplished gene searcher will also find this book a useful addition to their library - an excellent reference to the principles of bioinformatics." - Trends in Biochemical Science
"- a nice overview of - bioinformatics that is suitable for the neophyte and those experienced in the field - With the wide variety of topics covered, this book is one that should be included in the collection of anyone involved with the emerging field of bioinformatics." -Biotech Software and Internet Report


Pierre Baldi and Sÿren Brunak, Bioinformatics; The Machine Learning Approach
This book describes key machine learning approaches to molecular biology, including neural networks and hidden markov models. It is intended for two audiences: computer scientists / mathematicians and molecular biologists.


Pavel Pevzner, Computational Molecular Biology
In one of the first major texts in the emerging field of computational molecular biology, Pavel Pevzner covers a broad range of algorithmic and combinatorial topics and shows how they are connected to molecular biology and to biotechnology. The book has a substantial "computational biology without formulas" component that presents the biological and computational ideas in a relatively simple manner. This makes the material accessible to computer scientists without biological training, as well as to biologists with limited background in computer science.


M.J. Bishop and C.J. Rawlings (editors), DNA and Protein Sequence Analysis---A Practical Approach
IRL Press at Oxford University Press, 1997 ISBN 0 19 963464 5 (Hbk) ISBN 0 19 963464 7 (Pbk)
An excellent introduction to Internet resources for molecular biologists. Unique coverage of issues relating to analysis of genomic sequence data. Provides an overview of the science underlying modern bioinformatics tools. Deals explicitly with the issues of interpreting results from computer analysis of DNA and protein sequence - not just how to run the programs.


R. Durbin and S. Eddy and A. Krogh and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
Cambridge University Press.
A tutorial introduction to the use of hidden Markov models, stochastic context free grammars and other probabilistic models for sequence analysis problems in computational molecular biology.


W. Ewens and G. Grant, Statistical Methods in Bioinformatics
Springer-Verlag NY
This book grew out of a need to teach bioinformatics to graduate students at the University of Pennsylvania. At the same time however, it is organized to appeal to a wider audience. In particular it should appeal to any biologist or computer scientist who wants to know more about the statistical methods of the field, as well as to a trained statistician who wishes to become involved in bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, and will be accessible to students who have only had introductory calculus and linear algebra.


S.L. Salzberg, D.B. Searls, and S. Kasif (eds.), Computational Methods in Molecular Biology
Elsevier Science B.V., Amsterdam, 1998.
This book describes a range of different computational approaches to gene finding, protein structure prediction, and other sequence analysis problems. Tutorial material is included to make topics such as hidden Markov models accessible to the reader with a background in biology. Other tutorials are included to introduce biological concepts to readers whose background is computer science or something else besides molecular biology.


J. Setubal and J. Meidanis, Intro. to Computational Molecular Biology,
PWS Publishing Co., 1997.


M.S. Waterman, Introduction to Computational Biology
This book is intended to introduce someone who has advanced mathematical skills to the subject of biological data and problems.

C.H. Wu, Neural Networks and Genome Informatics
This book is a comprehensive reference in the field of neural networks and genome informatics. The tutorial of neural network foundations introduces basic neural network technology and terminology. This is followed by an in-depth discussion of special system designs for building neural networks for genome informatics, and broad reviews and evaluations of current state-of-the-art methods in the field. This book concludes with a description of open research problems and future research directions.


Proceedings of Intelligent Systems for Molecular Biology 1997
375 pages recounting the presentations and events of this critical conference which was held in Greece in 1997.


Michael J. E. Sternberg, editor, Protein Structure Prediction---A Practical Approach
Oxford University Press, London, 1996.
A very good introductory tutorial for molecular biologists. Covers Sequence databases, alignment and secondary & tertiary structure prediction.


Sequence Analysis Primer
Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the necessary background to enter this exploding field and helps more seasoned researchers to fine-tune their approach.

BioInform also has a large list of computational biology books, with links to ordering sites.

 

While ISCB does provide links to conferences, events, and other news items that may be of use to ISCB members and bioinformaticians at large, ISCB has no control over non-ISCB resources, and is not responsible for the content provided by outside sources. Such listings are not meant as an endorsement by ISCB.

Bioinformatics Books List


Over the years ISCB members and scientific publishers have notified us of books with specific relevance to our community of computational biologists. Below is a listing of those books, alpha by author, from which you can link to more detailed information with the option to also link straight to Amazon.com to make a purchase. If you are aware of a high quality book missing from our list, please write to This email address is being protected from spambots. You need JavaScript enabled to view it. and we will consider adding it soon.

  1. Descarga (The first book of Bioinformatics for Spanish speakers)
    Author(s):  F. Abascal, J. Aguirre, E. Andrés-León, D. Bajic, D. Baú, J. A. Bueren-Calabuig, Á. Cortés-Cabrera, I. Dotu, J. M.   Fernández, H. G. D. Santos, B. Garcı́a-Jiménez, R. Guantes, I. Irisarri, N. Jiménez-Lozano, J. Klett, R. Méndez, A. Morreale, A. Pascual-Garcı́a, A. Perona, A. Sebastian, M. Stich, S. Tarazona, I. Yruela y R. Zardoya
    Editor(s):  Álvaro Sebastián and Alberto Pascual-Garcı́a
  2. DNA Sequencing: From Experimental Methods to Bioinformatics
    Author(s): Luke Alphey
  3. Systems Bioinformatics: An Engineering Case-Based Approach
    Author(s): Gil Alterovitz and Marco R. Ramoni
  4. Text Mining for Biology and Biomedicine
    Editor(s): Sophia Ananiadou and John McNaught
  5. Introduction to Bioinformatics
    Author(s): Teresa Attwood, David Parry-Smith
  6. Ontologies for Bioinformatics
    Author(s): Kenneth Baclawski and Tianhua Niu
  7. Bioinformatics: The Machine Learning Approach
    Author(s): P.Baldi and S. Brunak
  8. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling
    Author(s): Pierre Baldi, G. Wesley Hatfield
  9. Bioinformatics for Geneticists
    Author(s): Michael Barnes, Ian C Gray
  10. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition
    Author(s): Andreas D. Baxevanis and B. F. Francis Ouellette (Eds)
  11. Bioinformatics Computing
    Author(s): Bryan P. Bergeron
  12. Genetics Databases
    Author(s): M. J. Bishop
  13. Problems and Solutions in Biological Sequence Analysis
    Author(s): Mark Borodovsky and Svetlana Ekisheva
  14. Structural Bioinformatics
    Author(s): Philip E. Bourne, Helge Weissig
  15. Computational Modeling of Genetic and Biochemical Networks
    Author(s): James M. Bower and Hamid Bolouri
  16. Bioinformatics: A Biologist's Guide to Biocomputing and the Internet
    Author(s): Stuart M. Brown
  17. Discovering Genomics, Proteomics, and Bioinformatics
    Author(s): A. Malcolm Campbell, Laurie J. Heyer
  18. Biological Database Modeling
    Editor(s): Jake Chen and Amandeep S. Sidhu
  19. Bioinformatics for Dummies
    Author(s): Jean-Michel Claverie and Cedric Notredame
  20. Computational Molecular Biology: An Introduction
    Author(s): Peter Clote, Rolf Backofen
  21. Introduction to Computational Genomics: A Case Studies Approach
    Author(s): Nello Cristianini and Matthew W. Hahn
  22. Bioinformatics (Methods Express Series)
    Author(s): Paul Dear
  23. Bioinformatics Algorithms: An Active Learning Approach, 2nd Edition, Vols. 1 and 2
    Author(s): Phillip Compeau, Pavel Pevzner
  24. Analysis of Microarray Data: A Network-Based Approach
    Editor(s): Matthias Dehmer and Frank Emmert-Streib
  25. Nonlinear Estimation and Classification
    Author(s): D.D. Denison, M.H. Hansen, C.C. Holmes, B. Mallick & B. Yu (Eds.)
  26. Biological Sequence Analysis
    Author(s): Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
  27. Genomic Perl: From Bioinformatics Basics to Working Code
    Author(s): Rex A. Dwyer
  28. Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis
    Author(s): Ingvar Eidhammer, Inge Jonassen, William R.T. Taylor
  29. Computational Cell Biology
    Author(s): Christopher P. Fall, Eric S. Marland, John M. Wagner
    and John J. Tyson, Editors
  30. Cluster and Classification Techniques for the Biosciences
    Author(s): Alan Fielding
  31. Evolutionary Computation in Bioinformatics
    Author(s): Gary B. Fogel, David W. Corne
  32. Mathematics of Evolution and Phylogeny
    Author(s): Olivier Gascuel (Editor)
  33. Reconstructing Evolution: New Mathematical and Computational Advances
    Author(s): Olivier Gascuel (Editor), Mike Steel (Editor)
  34. Bioinformatics: Principles & Applications
    Author(s): Zhumur Ghosh, Bibekanand Mallick
  35. Developing Bioinformatics Computer Skills
    Author(s): Cynthia Gibas, Per Jambeck
  36. Statistical Methods in Bioinformatics: An Introduction
    Author(s): Gregory R. Grant, Warren J. Ewens
  37. Algorithms on Strings, Trees and Sequences
    Author(s): Dan Gusfield
  38. Longitudinal Data Analysis
    Author(s): Hedeker Donald, Gibbons Robert D.
  39. Bioinformatics : Sequence, Structure, and Databanks : A Practical Approach
    Author(s): Des Higgins (Editor), Willie Taylor (Editor)
  40. Probabilistic Modelling in Bioinformatics and Medical Informatics
    Author(s): Dirk Husmeier (Editor), Richard Dybowski (Editor), Stephen Roberts (Editor)
  41. Current Topics in Computational Molecular Biology
    Author(s): Tao Jiang, Ying Xu and Michael Q. Zhang (Eds.)
  42. Current Topics in Computational Molecular Biology
    Author(s): Neil C. Jones and Pavel A. Pevzner
  43. Post-genome Informatics
    Author(s): Minoru Kanehisa
  44. Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems
    Author(s): Edward Keedwell, Ajit Narayanan
  45. Foundations of Systems Biology
    Author(s): Hiroaki Kitano
  46. Guide to Analysis of DNA Microarray Data
    Author(s): Steen Knudsen
  47. Microarrays for an Integrative Genomics
    Author(s): Isaac S. Kohane, Alvin Kho, Atul J. Butte
  48. Systems Biology: Principles, Methods, and Concepts
    Author(s): Andrzej K. Konopka (Editor)
  49. Compact Handbook of Computational Biology
    Author(s)
    : Andrzej K. Konopka (Editor), M. James C. Crabbe (Editor)
  50. BLAST
    Author(s): Ian Korf, Mark Yandell, Joseph Bedell
  51. Hidden Markov Models for Bioinformatics
    Author(s): Timo Koski
  52. Fundamental Concepts of Bioinformatics
    Author(s): Dan E. Krane, Michael L. Raymer
  53. Advances in Molecular Bioinformatics
    Author(s): Steffen Schulze-Kremer (Editor)
  54. Molecular Bioinformatics: Algorithms and Applications
    Author(s): Steffen Schulze-Kremer
  55. Computational Biology
    Author(s): Lecture Notes in Computer Science, Vol. 2066
  56. Analysis of Microarray Gene Expression Datas
    Author(s): Mei-Ling Ting Lee
  57. Bioinformatics: From Genomes to Drugs
    Author(s): Thomas Lengauer
  58. Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
    Author(s): Darryl Leon, Scott Markel
  59. Introduction to Bioinformatics
    Author(s): Arthur M. Lesk
  60. Computational Molecular Biology
    Author(s): J. Leszczynski
  61. Bioinformatics: Databases and Systems
    Author(s): Stanley Letovsky (Editor)
  62. Biomolecular Computation for Bionanotechnology
    Author(s): Jian-Qin Liu and Katsunori Shimohara
  63. Immunological Bioinformatics
    Author(s): Ole Lund, Morten Nielsen, Claus Lundegaard,
    Can Kesmir and Søren Brunak
  64. Intelligent Systems Modeling and Decision Support in Bioengineering
    Author(s): Mahdi Mahfouf
  65. Bioinformatics and Systems Biology: Collaborative Research and Resources
    Author(s): Frederick Marcus
  66. In Silico Technologies in Drug Target Identification and Validation
    Author(s): Scott Markel and Darryl Leon
  67. Computational Cell Biology
    Author(s): Eric Marland, John Wagner, John Tyson
  68. Bioinformatics and Genome Analysis
    Author(s): H.W. Mewes, B. Weiss, H. Seidel
  69. Bioinformatics: Methods and Protocols
    Author(s): Stephen Misener (Editor), Stephen A. Krawetz (Editor)
  70. Bioinformatics: Sequence and Genome Analysis
    Author(s): David W. Mount
  71. Foundations of Comparative Genomics
    Author(s): Arcady R. Mushegian
  72. Bioinformatics Algorithms: Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction
    Author: Enno Ohlebusch
  73. Bioinformatics: Genes, proteins and computers
    Author(s): C.A. Orengo, D.T. Jones and J.M. Thornton
  74. Algebraic Statistics for Computational Biology
    Author(s): Lior Pachter and Bernd Sturmfels
  75. Systems Biology: Properties of Reconstructed Networks
    Author(s): Bernhard O. Palsson
  76. Mathematics of Genome Analysis
    Author(s): Jerome K. Percus
  77. Computational Molecular Biology: An Algorithmic Approach
    Author(s): Pavel A. Pevzner
  78. A Beginner's Guide to Molecular Structures
    Author(s): Sandra Porter
  79. Exploring DNA Structure
    Author(s): Sandra Porter
  80. Bioinformatics Basics Applications in Biological Science and Medicine
    Author(s): Hooman H. Rashidi, Lukas K. Buehler
  81. Introduction to Computer-Intensive Methods of Data Analysis in Biology
    Author(s): Derek A. Roff
  82. The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
    Edited by Marco Salemi, Anne-Mieke Vandamme
  83. Computational Methods in Molecular Biology
    Author(s): S.L. Salzberg, D.B. Searls, S. Kasif
  84. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families
    Author(s): David Sankoff, Joseph H. Nadeau
  85. Molecular Modeling and Simulation: An Interdisciplinary Guide
    Author(s): Tamar Schlick
  86. Kernel Methods in Computational Biology
    Author(s): Bernhard Schölkopf, Koji Tsuda and Jean-Philippe Vert (Eds.)
  87. Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism
    Author(s): Dietmar Schomburg (Editor), Uta Lessel (Editor)
  88. Phylogenetics
    Author(s): Charles Semple and Mike Steel
  89. Introduction to Computational Molecular Biology
    Author(s): Joao Carlos Setubal, Joao Meidanis, Jooao Carlos Setubal
  90. Likelihood, Bayesian and MCMC Methods in Quantitative Genetics
    Author(s): Daniel Sorensen, Daniel Gianola
  91. Bioinformatics: Sequence Alignment and Markov Models
    Author(s): Kal Renganathan Sharma
  92. Microarray Bioinformatics
    Author(s): Dov Stekel
  93. Protein Structure Prediction - A Practical Approach
    Author(s): Michael J. E. Sternberg
  94. Computational Genomics: Current Methods
    Author(s): Nikola Stojanovic
  95. Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics
    Author(s): Gary D. Stormo
  96. Beginning Perl for Bioinformatics
    Author(s): James Tisdall
  97. Pathway Analysis and Optimization in Metabolic Engineering
    Author(s): Néstor V. Torres, Eberhard O. Voit
  98. Gene Regulation and Metabolism: Post-Genomic Computational Approaches
    Author(s): Julio Collado-Vides and Ralf Hofestadt
  99. Computational Analysis of Biochemical Systems A Practical Guide for Biochemists and Molecular Biologists
    Author(s): Eberhard O. Voit
  100. Coalescent Theory: An Introduction
    Author(s): John Wakeley
  101. Pattern Discovery in Biomolecular Data - Tools, Techniques, and Applications
    Author(s): Jason T. L. Wang, Bruce A. Shapiro, and Dennis Shasha
  102. Introduction to Computational Biology: Maps, Sequences and Genomes
    Author(s): Michael S Waterman
  103. Instant Notes Bioinformatics
    Author(s): D.R. Westhead, J. H. Parish, R.M. Twyman
  104. The Practical Bioinformatician
    Author(s): Limsoon Wong
  105. Neural Networks and Genome Informatics
    Author(s): Cathy H. Wu, Jerry W. McLarty
  106. Essential Bioinformatics
    Author(s): Jin Xiong
  107. Applications of Fuzzy Logic in Bioinformatics
    (Series on Advances in Bioinformatics and Computational Biology)

    Author(s): Dong Xu (Editor), James M. Keller (Editor), Mihail Popescu (Editor),
    Rajkumar Bondugula (Editor)
  108. Life Science Automation Fundamentals and Applications
    Editor(s): Mingjun Zhang, Bradley Nelson, and Robin Felder
  109. Understanding Bioinformatics
    Market Zvelebil

    List initially compiled by Aik Choon TAN

TOP


While ISCB does provide links to conferences, events, and other news items that may be of use to ISCB members and bioinformaticians at large, ISCB has no control over non-ISCB resources, and is not responsible for the content provided by outside sources. Such listings are not meant as an endorsement by ISCB

International Society for Computational Biology
Publishing Survey Results


August 13, 2004
Scholarly publishing is one of the major roles of a scientific society, to allow dissemination of research in the society's field. On August 3, 2004 the International Society for Computational Biology (ISCB) sent a survey via email to all of its members in an effort to include their input in the current evaluation of its journal affiliation. Below are the questions asked, corresponding results from the 197 member responses (approximately 10% of the current membership), and verbatim comments from all who responded by the August 13, 2004 deadline.

Current affiliation and approaches (197 responses)
ISCB has as its current official journal Bioinformatics, published by Oxford University Press under a traditional subscription publishing model with all articles freely available to the public via the OUP website 12 months after publication. A variety of additional journals are also available to ISCB members at a discounted rate, each with its own publishing model and levels of open access (see www.iscb.org/iscb-publications-journals for more details). Are you satisfied with the Society’s current scientific publishing mechanism and affiliation, or do you think it should be changed?
  1. Strongly prefer current affiliation and approach—46 (23%)
  2. Weakly prefer current affiliation and approach—49 (25%)
  3. Don’t care—18 (9%)
  4. Weakly prefer new affiliation and approach—39 (20%)
  5. Strongly prefer new affiliation and approach—35 (18%)
  6. Don’t know anything about current affiliation and approach—10 (5%)
48% strongly/weakly prefer current affiliation & approach
38% strongly/weakly prefer new affiliation & approach

Traditional subscription model versus open access (197 responses)

The subscription model of publishing involves publishers charging a fee for printed versions a journal (around $1000 for institutions, about $150 to individuals; free or discounted access to developing nations). These subscription fees pay the publisher’s costs in having the article reviewed, edited, typeset, and published. In this model, authors of papers pay modest or no page fees, as well as often charges for color figures (typically $500/page). The journal is exclusively available to subscribers for a period of at least six months after publication. This model minimizes costs to authors and has the “consumer” pay.

In the open access model, authors must pay a fee of $500-$1500 to cover reviewing, editing, typesetting. (Fee waivers are available to those without publication funds.) The article is freely available for all immediately upon publication. Paper versions may also be bought for the cost of printing. This model ensures everyone can access the articles and the research is immediately available for readers as well as text-mining, indexing, and redistribution (see http://www.nature.com/nature/debates/e-access/ for more information on open access). What is your preference?
  1. Strongly prefer traditional subscription model—29 (15%)
  2. Weakly prefer traditional subscription model—21 (11%)
  3. Don’t care—10 (5%)
  4. Weakly prefer open access—32 (16%)
  5. . Strongly prefer open access—105 (53%)
26% strongly/weakly prefer traditional subscription model
69% strongly/weakly prefer open access

Role of the Society in selecting editors (193 responses)

The scientific leadership of a journal comes from the Executive Editor (also called the Editor-in-Chief). What do you feel about the importance of the Society’s role in selecting an executive editor as well as other members of the editorial board?
  1. Prefer publisher solely select editors—9 (4%)
  2. Appropriate for publisher to select editors with Society input—44 (23%)
  3. Appropriate for both publisher and Society to jointly appoint editors—98 (51%)
  4. Feel it is necessary for Society to have ultimate control over editors—42 (22%)
Scientific Scope (188 responses)
In the Society’s current official journal, do you feel that the scientific scope is appropriate?
  1. The scope is too broad—7 (4%)
  2. The scope is appropriate—128 (68%)
  3. The scope is too narrow—36 (19%)
  4. Don’t know—17 (9%)
Comments (14 subject specific and 18 general comments received out of 197 total survey respondents)Specific Comments:
Added specifically after the question regarding current affiliation and approaches:
  • Hard to answer without information on possible new affiliation (selected option 2 to weakly prefer current affiliation and approach)
  • I guess 2 is my choice (Weakly prefer current affiliation and approach). I would like to see the ISCB to use its influence to have all the journals we associate with move to the open access model. I know that such costs will be prohibitory for some authors but I think the open access model is a better business model in the long run.
  • prefer current journals, but would like open access
  • Strongly prefer non-OUP
Added specifically after the question regarding traditional model vs open access preference:
  • with downloadable pdf's (selected option 5)
  • I guess 4 is my choice (Weakly prefer open access). I would like to see the ISCB to use its influence to have all the journals we associate with move to the open access model. I know that such costs will be prohibitory for some authors but I think the open access model is a better business model in the long run.
  • with strong focus on minimizing cost structure & maintaining availability for independent / under funded researchers (selected option 5 - Strongly prefer open access)
  • In principle would be 5 (Strongly prefer open access), but the current request for the authors are too high
Added specifically after the question regarding role of the society in selecting editors:
  • No preference, as long as the journal is doing a good job
Added specifically after the question regarding scientific scope:
  • It varies from issue to issue, I have not seen the latest yet
  • but not strongly, actually- the scope is not bad, currently (selected option 3 - The scope is too narrow)
  • Broad terms are used in the description of the scope but I'm not sure what subcategories fall within these terms. I would like to see phylogenetic analysis of genomic data through computational approaches added/included within the scope of the journal.
  • I would like to see more structure-related papers. Also more papers that describe joint experimental and computational work.
  • Too narrow. I would like to see more genomics of the type published in Genome Research (esp. the methods articles) in addition to the current algorithmic/software focus.
General Comments:
  • Thank you very much for seeking input from members, I hope the results will be available too.
  • I think that we (ISCB) should do everything that we can to encourage any of the publishers that were are affiliated with to release articles within 6 months of publication. And to strongly encourage completely open access.
  • The Society may which to have 2 official journals: one traditional and one open-access. It is vitally important that
    1. we do not support one of the "rip-off" publishers that sets astronomically high fees for libraries and never provides free access
    2. the quality of the scientific content of the journal is kept as high as possible, even at the expense of smaller publications. We do not our name associated with "bottom-feeder" journals.
    3. cost be kept reasonable
    4. archives that can be kept for at least 50 years are guaranteed (a potential problem with open-access, electronic-only journals---what happens to the content if the publisher fails?)
  • Please strongly consider going to the open access model. As a person who often works with small biotechnology firms, and no current academic affiliation, it is very difficult and expensive to get access to quality journal articles.
  • I would like to see additional sections in the "official" journal dealing with non-scientific interests: academic articles, running bioinformatics core centers, etc.
  • The open access model is very attractive at first sight. But, on the long run it will have to demonstrate its effectiveness (e.g.: Is the economic model really sustainable for the huge number of scientific publication existing to date? ...). So we should not a priori highly rate this model. We need to see how it stands with our expectations when it really faces the real world constraints.
  • On open access journals: The fees charged for current open access journals seem prohibitively high for any but very well-funded researchers to be able to seek publication. I would favor moving to an open access model for Society journals if and only if a way can be found to reduce the price per article to a level that brings it within the reach of grad students and less-well-funded researchers. As a rule of thumb, the price per article for an open access journal should be no greater than the price of a year's individual subscription to a traditional journal.
  • On journal subscriptions: The message "At the moment you are not able to upgrade your subscriptions. We hope to have this option available soon." has been on the subscriptions management page (https://www.iscb.org/mem_new_journal.php) for some time ... Members should be able to change subscription status at any time.
  • I think there should be
    1. a New Programs, Website, and Databases section, to be published online only. Currently, much too many announcements of new tools end up in print, with many of them being obsolete by the time they are published
    2. a Methods section that can have a broad scope of both in-silico only methods and also approaches that are closer to the wet-lab. This could either be in print or also online only (like the NAR methods section)
    3. if the journal is not Open Access, then the very least ISCB should negotiate is free online access for its membership (the way it used to be with Bioinformatics).
  • I would like to see Bioinformatics focus more on biological information rather than the bioinformatics of biology. By this I mean that papers dealing with the passage of genetic information from the genome to the proteome and to the structure and function of macromolecules and eventually to the phenotype of the organism are more fundamental than papers dealing with LIMS systems or instrumentation. I would like the biology to be more central to papers in the future.
  • A serious problem with the journal Bioinformatics is the time the journal takes from review to publication. From my experience, and the one of colleagues, it appears that a one year delay from submission to the time the article appears in press is not unusual, and this is just plainly unacceptable in a field that moves at a fast pace.
  • While I support an alternative, free access model, I strongly object to the proposed open-access model in which authors paying for publishing. It is both unfair to the authors who already pay for the research from grant money and put a lot of work and time into the writing and editing process. I also believe it can promote a "rich"-group-dominated science, publishing many small papers, while leaving little choice for "outsiders" and/or "poor" authors. Moreover, currently an author can buy the pdf from "conventional" journals and put it online individually, for a fraction of the open-access costs. I believe text should be freely available, but also believe that the financing model should be based on commercial sponsors and possibly advertisements, or special services provided for additional cost (e.g. a particularly effective search engine, hard copies, special copy editing services for authors etc.)
  • I think that the subscription to Bioinformatics should be available to ISCB members at a discounted rate.
  • In my view the open access model is the right one for 21'st century scientific publishing. The major public scientific societies should move as soon as possible to this model, since it truly disseminates scientific knowledge in real time. Having said that, it is important to keep the publishing fee low, since the costs of web publishing are minimal and the refereeing is done by volunteers. It is unthinkable, that a young scientist would be unable to publish his/her work due to high publication fees. To avoid this two major steps should be undertaken:
    1. There should be an Institutional publishing fee, so, that all the researchers in a University/Institute paying such a fee would be exempt from a personal publishing fee. This fee should be relatively low, comparable to an institutional journal subscription fee.
    2. Granting agencies, such as NSF, EU program, and national science foundations should be encouraged to appropriate grants in support of open access publications, based on the quality and scientific relevance of the journals. This could be an excellent opportunity both to encourage free dissemination of scientific ideas and both to preserve the high scientific quality of the web-based publications.
  • I think it would be unfortunate if ISCB terminated its association with Bioinformatics. I think the journal has done a lot for the field and for the society and I am pleased with the move toward open access. While I am a strong supporter of open access, I understand the financial constraints that Bioinformatics faces as OUP does not have the same sort of grant funded cushion that PLOS has. On the other hand, I do not think it would be inappropriate for the society to be affiliated with more than one journal. Bioinformatics could retain its focus but a new, more biologically focused journal that also emphasized computational approaches might allow us to reach a larger audience.
  • The current content-owned-by-publisher model makes it impossible to do full text open searches for content, needed for all sorts of plain text informatics searching. We must switch to a full open access model and stop giving our copyright to publishers who restrict access.
  • I am skeptical that open access will be a good way to change publishing in all the different sciences -- the cost of publishing is often shifted from the university/library as a whole to the individual research groups, which may often be problematic. However, I would strongly encourage journals to make their articles free of charge after a period of 6-12 months, the shorter the better, as it has already happened with some journals.
  • I feel that the Bioinformatics journal has a broad scope. This makes sense, since the field of Bioinformatics is broad as well. I should also wish to bring to your attention the fact that several colleagues frequently publish their research achievements and results in other journals. This is due to the fact that some specialized papers fit well into other journal's scope (or are probably of a wider interest) or that the Bioinformatics journal cannot hold all this huge nubmer of submitted papers, even though the last couple of years the number of issues per volume have substantially been increased. Well established journals specialized in other (marginally) related fields often publish special issues related to Bioinformatics (e.g. the NAR Database and Web-Server Issues). Perhaps, the ISCB could establish contacts with more publishers and Journals on Computational Biology/Bioinformatics. This could raise the impact/prestige of these journals, providing high quality alternatives for publishing or gaining access to specialized research in our field.

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ISMB Proceedings

ISCB is pleased to have the following ISMB Proceedings available:

ISMB Proceedings from the 1993-2000 ISMB conferences are available to ISCB Members through the American Association for Artificial Intelligence (AAAI Press). Links below directly access AAAI's ISMB Proceedings pages by year.

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NIH Public Access Policy Member Poll

Dear ISCB members and colleagues,

In 2008 the U.S. Congress required the National Institutes of Health to implement a Public Access Policy that requires investigators funded by the NIH to submit, or have submitted for them, an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to the National Library of Medicine's digital archive, PubMed Central, to be posted publicly within 12 months after the official date of publication. (See http://edocket.access.gpo.gov/2009/E9-3442.htm for the full notice and analysis of this NIH policy.)

Similarly, in England the Wellcome Trust implemented a like-minded policy for investigators funded with its resources, and in Germany the Max Planck Society committed to paying for all open access publications from any of its institutes.

A new bill, HR 801, was recently introduced in the U.S. House of Representatives, to prohibit any U.S. federal agency from mandating a public access policy as a condition of funding.

Supporters of open access are taking a strong position against HR 801, while organizations that stand to benefit from limiting or eliminating the current NIH policy are standing in favor of the bill.

Members of the senior leadership of ISCB support the current NIH Public Access Policy, and are therefore opposed to HR 801. However, before making any public statements on this issue in the name of ISCB, we are seeking your input. Even if you are not a U.S. citizen or live and work outside of the U.S., your input is important in helping guide ISCB's next steps on this topic.

Please click here to participate in the brief poll to help determine if ISCB shall make a public statement on this issue.

ISCB members are eligible to receive exclusive subscription/publishing discounts to the following journals related to the bioinformatics and computational biology community:

Other publications that may be of interest to ISCB Members include the following (discounts do not apply, although some are free upon registration or open access):


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Exclusively for members

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    ISCB Members enjoy discounts on conference registration (up to $150), journal subscriptions, book (25% off), and job center postings (free).

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