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Table of Contents: February 2014

COVER

The Speed Boat activity: using interactive games to inspire creativity and explore challenges 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.
Issue Image

"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.

Editorial

Ten Simple Rules for Running Interactive Workshops

Katrina Pavelin, Sangya Pundir, Jennifer A. Cham

Message from ISCB

Workshops: A Great Way to Enhance and Supplement a Degree

Segun Fatumo, Sayane Shome, Geoff Macintyre

Perspectives

Combining Experiments and Simulations Using the Maximum Entropy Principle

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

A Unified View of “How Allostery Works”

Chung-Jung Tsai, Ruth Nussinov

Research Articles

tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria

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

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

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

Pascal Carrivain, Maria Barbi, Jean-Marc Victor

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

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

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

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

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

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

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

Mathematical Modeling of the Phoenix Rising Pathway

Chad Liu, Chuan-Yuan Li, Fan Yuan

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