Author: Chris Hall

Stories from the road: Trials and tribulations of the ISCB Student Council

The Student Council for the International Society for Computational Biology was established in 2004 to promote the development of computational biology among young scientists. The group runs events and programmes, as well as supporting the creation of Regional Student Groups.

Image Credit: Vignesh GPAs an official journal of the ISCB, PLOS Computational Biology is delighted to be publishing ‘Stories from the road: ISCB Student Council Collection’, a series of articles documenting the various activities of the ISCB student community and providing guidance to future generations of ISCB Student Council members. From the importance of creating a culture where networking is possible, to tips for workshopping ideas and problems, the series captures the experiences of young scientists.

“Collaborating with authors and contributors from dozens of countries around the globe has been an extremely interesting, challenging and rewarding experience,” says Thomas Abeel, one of the authors of the series. “Putting this series together has brought back some great memories, reinforced friendships and has re-taught some of the lessons we highlighted in these articles all over again.”

The collection’s primary authors and organisers were Thomas Abeel, Geoff Macintyre and Magali Michaut. Their own account of the council and the creation of the collection can be read here.

It is the journal’s hope that this collection will help spread some of the wisdom that the council has acquired over the course of a decade.

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Modelling arterial hypertension, using the human genome in drug discovery and lessons from professional basketball: The PLOS Comp Biol May issue

Here is our selection of PLOS Computational Biology highlights for May.

Getting to know you: Innate immune sensing of fungal pathogen surfaces. Image Credit: Matthew S. Graus, Aaron K. Neumann

Getting to know you: Innate immune sensing of fungal pathogen surfaces. Image Credit: Matthew S. Graus, Aaron K. Neumann

No man ever steps into the same river twice, for it’s not the same river and he’s not the same man (Heraclitus of Ephesus, 535–475 BCE).  This is how Yonatan Lowenstien and Tal Neiman introduce their paper, “Spatial Generalization in Operant Learning”: Lessons from Professional Basketball”. The paper looks at operant learning and how behaviours are not reinforced or inhibited by the “same” actions, but instead by similar events, as in natural environments the “same” situation never occurs. While this is a familiar generalisation, the computational principles that underlie it are not fully understood, so the paper used statistics from professional basketball to study these principles. It was found that players are more likely to attempt a field goal from the vicinity of a previously made shot than they are from the vicinity of a missed shot. This result indicates that rather than using low-level features, operant learning in basketball is determined by high-level cognitive processes that incorporate the abstract rules of the game.

Genome-Wide Association Studies can provide great understanding for the etiologies of many complex diseases and have the potential to inform the discovery of safe and effective medicines. However, authors Lei Xie et al. write in their Review that these data have not been fully explored in order to improve the efficiency of drug discovery. The Review studies the dynamics of molecular interactions for the entirety of the human genome and shows that progress is being made towards the final goal of personalised medicines for the treatment of complex diseases.

Despite arterial hypertension, or high blood-pressure, being one of the most common age-related chronic disorders, its major cause remains enigmatic. Klas H. Pettersen et al. developed a computer model of the circulatory system; using this they demonstrate that arterial stiffening seems sufficient to explain age-related emergence of hypertension. The stiffening causes the blood-pressure sensors in the arterial wall to misinform the highly complex machinery responsible for blood pressure regulation.

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Detecting cancer-causing genes, computing how to beat jetlag and a review of research into decision-making: The PLOS Comp Biol April issue

Here is our selection of PLOS Computational Biology highlights for April.

Computer-based multi-client game for investigating human group movement. Image credit: Johannes Pritz, Courant Research Centre Evolution of Social Behavior, University of Gõttingen, Germany.

Computer-based multi-client game for investigating human group movement. Image credit: Johannes Pritz, Courant Research Centre Evolution of Social Behavior, University of Gõttingen, Germany.

Computational prediction of cancer-associated single nucleotide polymorphisms (SNPs) from SNP datasets can now be used as a tool for detecting probable cancer-causing genes. This work, by Rituraj Purohit et al., applies computational tools to prioritize the most harmful disease associated mutation in Aurora kinases. Sequence and structural based approaches were used to refine cancer associated mutation, and a long-term simulation (MDS) was applied in order to understand the changes in structural conformation and function of the aurora kinases upon mutation. Out of 60 SNPs, 24 were calculated to be deleterious as well as damaging.

Two papers we published in April received widespread attention in the media. The first paper, by Daniel Forger et al., presents a mathematical model for dealing with the effects of jet lag. By calculating thousands of schedules, the authors show how the human circadian pacemaker is capable of shifting much more rapidly than previously thought, simply by adjusting the timing of the beginning and end of each day. You can read the New Scientist article here.

The second paper to gain attention, by David J. McIver and John S. Brownstein, estimated levels of influenza in America by monitoring Internet traffic on specific Wikipedia articles. The developed model can accurately estimate the percentage of Americans with influenza-like illnesses in real-time. You can read more about it in this article by the Huffington Post

Despite the research that has gone into the workings of decision-making, the neural mechanisms underlying these processes are not fully understood. This Review article by Ranulfo Romo et al. looks at the recent progress made in this field of study and performs a critical evaluation of the available results from a computational perspective. The study was guided by a central question, which was “how does the spatiotemporal structure of sensory stimuli affect the perceptual decision-making process?

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The dynamical relationship of brain structure and function, environmental factors affecting autism and a budgie’s flight path: the PLOS Comp Biol March issue

Here is our selection of highlights published in PLOS Computational Biology for March.

Using mathematical models to design better anti-arrhythmic drugs. Image Credit: Megan Cummins, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

Using mathematical models to design better anti-arrhythmic drugs.
Image Credit: Megan Cummins, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

The relationship between brain structure and function is a central endeavour for neuroscience research, but the mechanisms that shape this relationship are highly debated. Authors Arnaud Messé et al. addressed this issue by systematically comparing functional connectivity taken from imaging data with simulations from increasingly complex computational models. The study demonstrates the existence of a dynamical regime in the brain that appears to be largely induced and shaped by the underlying anatomy. It also revealed that the critical importance of specific anatomical connections in shaping the global anatomo-functional structure of this dynamical regime, notably connections between hemispheres.

One paper from our March issue was featured in the news. The first looked at the environmental factors affecting autism by analysing the spatial incidence patterns of autism and intellectual disability drawn from insurance claims for nearly one third of the total US population. Authors Andrey Rzhetsky et al. found strong statistical evidence that environmental factors drive the apparent spatial heterogeneity of both phenotypes. Read the New Scientist article about it here.

Another of this month’s papers investigated the means by which birds choose routes while flying in cluttered environments. Budgerigars were trained to fly through a tunnel that gave them a choice of two routes. When one of the passages was substantially wider than the other, the birds tended to fly through the wider passage, regardless of whether this passage was on the right or the left. Bhagavatula et al. developed a mathematical model of the interaction between the birds’ individual biases with their tendency to prefer the wider passage. The model reveals that this interplay is beneficial for expediting the passage of a flock of birds through a complex environment. A video of one of the experiments can be found here.

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Dynamics of leadership in dog packs, communication in the cerebral cortex and modelling anti-tumour immunity: the PLOS Comp Biol January issue

Here is our selection of highlights for PLOS Computational Biology’s January issue.

PLOS Comp Biol Featured Image for January. Image Credit: Zsuzsa Ákos & Máté Nagy

PLOS Comp Biol Featured Image for January. Image Credit: Zsuzsa Ákos & Máté Nagy

The movement of a pack of Hungarian Vizslas was tracked by researchers from Oxford University and the Hungarian Academy of Sciences using high-resolution GPS harnesses in order to determine the dynamics of leadership roles, individual social ranks and personality traits. The authors found that the dogs’ movements were measurably influenced by underlying social hierarchies. Dogs that consistently took the lead were more responsive to training, more controllable, older and more aggressive than the dogs that tended to follow.

A fundamental question in systems neuroscience is how the structural connectivity of the cerebral cortex shapes global communication. More specifically Bratislav Mišić et al. found that much of global communication was mediated by a “rich club” of hub regions, which are areas of the brain comprised of densely interconnected nodes. The paper describes how these regions attract the most signal traffic and have more connections than non-rich club regions. Furthermore, a number of these regions were significantly under-congested, which suggests how connectivity can actively shape information flow. Overall, the results reveal a dynamic aspect of the global information processing architecture and the critical role played by the so-called “rich club” of hub nodes.

Recent advances in cancer immunotherapy stem from increasing the number of tumour-infiltrating immune cells, which is accomplished by inhibiting immune checkpoints or adoptive T cell therapy. David J. Klinke used computational methods to identify potential mechanisms present within the tumour microenvironment that limit the efficacy of anti-tumour immunity. The results will help identify design constraints for engineering better pre-clinical models of breast cancer.

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Reviewing software and code: an update

On June 14th 2013 Mozilla Science Lab announced their collaboration with PLOS Computational Biology. The collaboration was a trial series of software reviews conducted by Mozilla engineers for small pieces of code from articles already published with PLOS Computational Biology. The project began amidst discussion about the presentation of scientific code, such as this piece by Carl Boettiger, who stated: “We are not really taught to review software, any more than we are taught to write it in the first place.”

The project was spearheaded by Kaitlin Thaney from Mozilla Science Labs and Greg Wilson from Software Carpentry and announced by posts on Kaitlin’s blog and on PLOS Biologue. The full results have now been released on arXiv and summarised on the Mozilla Science blog, which explains that many of the scientists had never had their code reviewed before. Kaitlin states that while “the scientists aimed to produce readable, re-usable code, the reviewers felt their software was less reusable by others”. However, she also concludes that “the authors still found the comments useful, particularly feedback on usability, ease of re-use, organization of README files, code structure, performance questions and optimization”.

Since the first results were revealed, Mozilla Science Labs have announced that they are embarking on a second round of code reviews. In this version of the project, mentors from Mozilla will work with small groups of scientists, at first performing code reviews but also training the scientists to do the reviews themselves. Anyone who is interested in taking part as either a mentor or part of a team should use this email to get in touch.

It should be noted that this was a small-scale experiment and so much of the evidence provided is anecdotal. However, we believe that scientific research could benefit from an increase of these kinds of interactions. Overall we at PLOS Computational Biology are thrilled to have been a part of this project and hope that the results contribute to the growing world of scientific software.

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