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Table of Contents: February 2014

"Speed Boat" is a quick and easy activity to use as part of an interactive workshop. It helps your participants identify what improvements need to be made to a project, tool or process. It also reveals obstacles to reaching the desired goal. In this graphic, the boat represents the key issue to be addressed and the anchors are the challenges. The 'wind' arrows flanking the boat represent positive factors that move the project forward. Interactive games, such as those described in Pavelin et al., encourage creative thinking around a shared set of challenges, and are useful for stimulating problem-solving ideas in computational biology.

Image Credit: Jennifer A. Cham and the EMBL-EBI Industry Programme Agri-Food Workshop participants. Adapted from an activity described in Gamestorming by Gray et al.

Editorials

Ten Simple Rules for Running Interactive Workshops

Katrina Pavelin, Sangya Pundir, Jennifer A. Cham

Messages from ISCB

Workshops: A Great Way to Enhance and Supplement a Degree

Segun Fatumo, Sayane Shome, Geoff Macintyre

Perspectives

A Unified View of “How Allostery Works”

Chung-Jung Tsai, Ruth Nussinov

Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration

Tapesh Santra, Walter Kolch, Boris N. Kholodenko

Combining Experiments and Simulations Using the Maximum Entropy Principle

Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen

Research Articles

Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint

Germán Enciso, Douglas R. Kellogg, Arturo Vargas

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery

Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas

Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia

Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard

Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations

Florian Lesaint, Olivier Sigaud, Shelly B. Flagel, Terry E. Robinson, Mehdi Khamassi

Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms

Alan E. Bilsland, Katrina Stevenson, Yu Liu, Stacey Hoare, Claire J. Cairney, Jon Roffey, W. Nicol Keith

Mathematical Modeling of the Phoenix Rising Pathway

Chad Liu, Chuan-Yuan Li, Fan Yuan

The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer

Saliha Ece Acuner Ozbabacan, Attila Gursoy, Ruth Nussinov, Ozlem Keskin

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor

Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Elad Noor, Arren Bar-Even, Avi Flamholz, Ed Reznik, Wolfram Liebermeister, Ron Milo

A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain

Shyam Srinivasan, Jia Sheng Hu, D. Spencer Currle, Ernest S. Fung, Wayne B. Hayes, Arthur D. Lander, Edwin S. Monuki

A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood

Kerstin Hünniger, Teresa Lehnert, Kristin Bieber, Ronny Martin, Marc Thilo Figge, Oliver Kurzai

A Network Characteristic That Correlates Environmental and Genetic Robustness

Zeina Shreif, Vipul Periwal

A Unified Model of Heading and Path Perception in Primate MSTd

Oliver W. Layton, N. Andrew Browning

tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria

Katherine C. H. Amrine, Wesley D. Swingley, David H. Ardell

Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups

Thomas Garcia, Leonardo Gregory Brunnet, Silvia De Monte

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

Pascal Carrivain, Maria Barbi, Jean-Marc Victor

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes

Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino, Michele Caselle

A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses

Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel