{ C O N T E N T S }
Volume 11, Issue 1

President’s Letter

SCS4 Highlights

ISCB Honors
David Haussler
& Aviv Regev

The ISMB Organization
& Future Vision

PLoS Computational Biology Overview

11th Israeli Bioinformatics
Symposium Report

Taking a Stand on Software Sharing

ISCB Members Speak Out on US Entry Visa Issues

ISCB’s New Software
Sharing Statement


ISCB Student Council

Post Your Events with ISCB

MentorNet Report Card: Year Two

Calling all Leaders!

Become an ISMB Reporter

In Memory of
Kamalakar-Rao Mettani

FASEB Update

Rocky ‘08

Key Dates for Key Conferences

Conferences & Events

Cover Image




Copyright © 2008
International Society for
Computational Biology.
All rights reserved.


PLoS Computational Biology Overview

PLoS Computational Biology is now moving into its third year of publishing in association with the ISCB and we are pleased to see the positive reception of the community for this young but successful journal that is proving to positively impact the field of computational biology. We recently received our second impact factor of 6.236 from Thomson Reuters, placing us at the top of the Mathematical and Computational Biology category for the second year in a row
(see http://www.plos.org/cms/node/366 for PLoS’ view on impact factors). This statistic simply reflects the over 200 high-quality research articles published this year, showing the diversity and depth of the journal and, based on user statistics, a wide-ranging readership.

Three of the top ten downloaded articles are in the area of neurobiology. Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning by Manoonpong, Geng, Kulvicius, Porr and Worgotter, illustrates attempts to mimic human neurobiology. A hybrid and adaptive mechano–neuronal design strategy was used to build and control a small, fast, biped walking robot and to make it learn to adapt to changes in the terrain. Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences by Zhaoping and Jingling suggests that cortical areas beyond the primary visual cortex are responsible for visual inferences. Similarly, What Are Lightness Illusions and Why Do We See Them by Corney and Lotto provides causal evidence that illusions (and by extension all percepts) represent the probable source of images in past visual experience, which has fundamental consequences for explaining how and why we see what we do.

The fourth most downloaded article is that by Scheef and Bourne, who explore the Structural Evolution of the Protein Kinase–Like Superfamily. Published three years ago, this work benefits from the visibility and accessibility offered by its dissemination beyond journal publication by www.scivee.tv. At the time of writing, the authors’ pubcast – a video about the research integrated with the online content of the open access article -- has been viewed over 120,000 times and has led people to download the article PDF.

As a complement to the published research, PLoS Computational Biology has expanded the Education section of the journal guided by Education Editor and ISCB Education Committee Co-Chair Fran Lewitter. Key to this growth has been the publication of many of the Tutorials presented at ISMB meetings in 2006 and 2007. Designed to be practical, quick reference guides, these Tutorials are proving helpful for younger scientists and for anyone learning new methods or exploring the use of new tools. Published subjects range from Python to Bayesian networks to computational proteomics to the regulation of gene expression; all are available, along with previously published review articles, in the PLoS Computational Biology Education Collection at http://collections.plos.org/ploscompbiol/education.php.

In October of 2007, the journal and ISCB launched the “Getting Started in…” series under the editorial leadership of Olga Troyanskaya. These are short, practical articles written by experts for students and active researchers who want to learn more about new areas of computational biology but are unsure where or how to start. The first expert to inform, motivate, and inspire readers to consider a new direction was Dr. Xiaole Shirley Liu, who outlined the essentials of tiling microarray analysis. Then followed excellent introductions to text mining by Kevin Cohen and Larry Hunter, probabilistic graphical models in biology by Edo Airoldi, and analysis and modeling of biological pathways by Ganesh Viswanathan, Stuart Sealfon, and colleagues. The series now includes these four excellent articles, with more yet to come, including plans to cover topics ranging from biomedical databases to modeling in immunology. To read each of the current articles and keep up on others as they are published go to www.ploscompbiol.org and type “Getting Started in” in the search box. Our hope is that we have, and will continue, to inspire readers to consider new and exciting research directions.

“RunBot”, a neural controlled robot, demonstrates dynamic, biped walking, http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030134. Dynamic, biped walking is a difficult motor coordination problem for robots. “RunBot,” is equipped with actuators that are dynamically controlled by a neural network that can adapt via simulated synaptic plasticity to a change in terrain.