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.

Category: Bioinformatics, Computational biology, Open access, PLOS Computational Biology | Tagged , , , | Leave a comment

A huge thanks to our reviewers in 2013


Image credit ‘Todd’ on flickr

As 2014 begins we’d like to take the time to thank those who made it possible, including our fantastic peer reviewers.  In 2013 1199 people reviewed for PLOS Biology, 3780 in PLOS Genetics, and 2445 for PLOS Computational Biology. These generous individuals donated their time to assessing and improving our authors’ submissions. Their combined efforts have helped the PLOS biological journals (PLOS Biology, PLOS Genetics and PLOS Computational Biology) publish a fantastic and varied array of papers in 2013, amassing  6379364 online views and 673691 pdf downloads of articles so far!

We thank our reviewers for contributing their knowledge to the Open Access corpus. We here at PLOS would like to raise a toast to these amazing individuals. Without their critical insight, support, and hard work we couldn’t do what we do.

We’d also like to draw attention to the folks who have reviewed for the other PLOS journals:

PLOS ONE reviewers:

PLOS Medicine, PLOS Pathogens and PLOS Neglected Tropical Diseases reviewers:

Thanks again!


Category: Uncategorized | 1 Comment

Modelling protein interactions, tracing sources of infection, stem cell timescales and mammalian navigation: the PLOS Comp Biol December issue

Here is our selection PLOS Computational Biology highlights for December.

PLOS Comp Biol Featured Image for December. Image Credit: Image Credit: Andreas Bunten and clix

PLOS Comp Biol Featured Image for December. Image Credit: Andreas Bunten and clix

One of the challenges in cancer research is inadequate understanding about the coordinated interactions between signalling proteins. Drugs specifically designed to target effects of these proteins are promising agents and so authors Chris Sander et al have developed a method adapted from statistical physics, called Belief Propagation. This method calculates the most likely interactions amongst all other potential solutions. The results have the potential to model the effects of hundreds of proteins on cellular responses.

Molecular data from pathogens may be useful for identifying sources of infection and identifying which host transmitted to the other. However, the source of transmission is often complicated by numerous factors, so Erik Volz et al present a method that incorporates additional information about infectious epidemics such as incidence and prevalence of infection over time. This informs estimates of the probability that one sampled host is the direct source of infection of another host in a pathogen gene genealogy.

Stem cells are known for their phenotypic heterogeneity and cell-to-cell variation. A new paper, entitled “Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells” analyses this phenotypic variation by simulating the stochastic dynamics of gene networks in embryonic stem cells. The researchers found that identifying the distribution of timescales of these processes is vital to the characterisation of the dynamical behaviour of the gene network.

Navigation in mammals is a well-studied area both behaviourally and neurophysiologically. Using computational neuroscience, researchers Will D. Penny et al created a probabilistic model to support multiple tasks such as computing a sequence of motor commands. The authors propose that these computations are reflected in recent findings of pattern replay in the mammalian brain.

By Chris Hall, Senior Publications Assistant, PLOS Computational Biology

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Will Stem Cell Therapy Help Cure Spinal Cord Injury?

Experimental spinal injury in a mouse (DOI: 10.1371/journal.pone.0017126)

Experimental spinal injury (dark area) in a mouse (DOI: 10.1371/journal. pone.0017126)

Spinal cord injuries are mostly caused by trauma, often incurred in road traffic or sporting incidents, often with devastating and irreversible consequences, and unfortunately having a relatively high prevalence (250,000 patients in the USA; 80% of cases are male). High-profile campaigners like the late actor Christopher Reeve, himself a victim of sports-related spinal cord injury, however, have placed high hopes in stem cell therapy.

Stem cell therapy involves administering special self-regenerating cells (“stem cells“), with the hope that these cells will then colonise the damaged area, assume the properties of their neighbours and reinstate at least some of the function that’s been compromised by injury or disease. Stem cells have to be isolated from the patient or a donor, or generated afresh by tricking ordinary non-regenerating cells into becoming stem cells. Stem cell therapy has become fairly standard for re-colonising bone marrow that has been ravaged by cancer chemotherapy, but its application to other damaged tissues, including spinal cord injury, is still very much at the experimental stage.

In using stem cells for spinal cord injury, scientists are looking to repopulate damaged areas of the spinal cord (see the picture above), with the hope of improving the ability of patients to move (“motor outcomes”) and to feel (“sensory outcomes”) beyond the site of the injury. Many studies have been performed that involve animal models of spinal cord injury (mostly rats and mice), but these are limited in scale by financial, practical and ethical considerations. These limitations hamper each individual study’s statistical power to detect the true effects of the stem cell implantation. As explored previously on Biologue, there are also problems of bias (“It’s official – the animal study literature is biased… but whose fault is it?“).

Flickr user kittenfc

Lab rats (Image credit: Flickr user kittenfc)

How can we get round these shortcomings and find out how likely it is that stem cell therapy will improve the lot of spinal cord injury patients? This is the question addressed in a paper just published in PLOS Biology by Ana Antonic, David Howells and colleagues. They overcame the problem by conducting a “meta-analysis” – a sophisticated and systematic cumulative statistical reappraisal of many previous laboratory experiments. In this case the authors assessed 156 published studies that examined the effects of stem cell treatment for experimental spinal injury in a total of about 6000 animals.

Overall, they found that stem cell treatment results in an average improvement of about 25% over the post-injury performance in both sensory and motor outcomes, though the results can vary widely between animals. For sensory outcomes the degree of improvement tended to increase with the number of cells introduced – scientists are often reassured by this sort of “dose response”, as it suggests a real underlying biologically plausible effect. So the good news is that stem cell therapy does indeed seem to confer a statistically significant improvement over the residual ability of the animals both to move and feel things beyond the spinal injury site.

The authors went on to use their analysis to explore the effects of bias (such as whether the experimenters knew which animals were treated and which untreated), the way that the stem cells were cultured, the way that the spinal injury was generated, and the way that outcomes were measured. In each case, important lessons were learned that should help inform and refine the design of future animal studies. The meta-analysis also revealed some surprises that should provoke further investigation – there was little evidence of any beneficial sensory effects in female animals, for example, and it didn’t seem to matter whether immunosuppressive drugs were administered or not.

The authors conclude: “Extensive recent preclinical literature suggests that stem cell-based therapies may offer promise; however the impact of compromised internal validity and publication bias means that efficacy is likely to be somewhat lower than reported here.”
Ana Antonic, Emily S. Sena, Jennifer S. Lees, Taryn E. Wills, Peta Skeers, Peter E. Batchelor, Malcolm R. Macleod, & David W. Howells (2013). Stem Cell Transplantation in Traumatic Spinal Cord Injury: A Systematic Review and Meta-Analysis of Animal Studies PLoS Biology, 11 (12) DOI: 10.1371/journal.pbio.1001738

Category: Biology, Neuroscience, PLOS Biology, Research, Stem cells | 3 Comments

Outside the Box – Get Involved

How are computational methods being used across disciplines? PLOS Computational Biology Founding Editor-in-Chief Phil Bourne calls for examples.

An advantage of being a part time university administrator (there are lots of disadvantages) is that you meet a larger diversity of people on your campus than you would as a professor working in one research area. One such encounter has led to something I think is new and exciting for PLOS Computational Biology. I was at our Rady School of Management at UCSD talking to a faculty member when suddenly he quotes a paper from PLOS Computational Biology and says, “I use a statistical method from this paper in my business analytics work doing a market analysis for a major corporation.” Bingo! An example of ‘Outside the Box’ – computational biology tools being used in unimaginable ways in disciplines I would never have dreamed of.

What other examples are out there? We already have a handful, but need your help in starting an exciting PLOS initiative that demonstrates the broad reach of computational biology. Please be in touch suggesting names of authors and let me know if you might have an interest in helping edit such a series. Use of tools from phylogenetic analysis to derive the lineage of ancient texts is just one other example we have unearthed. Cool stuff – help us find more and let me know at

Category: Community, Computational biology, Research, Resources | Tagged , , | Leave a comment

The Changing Face of Education at PLOS Computational Biology

In January 2006, Fran Lewitter, PLOS Computational Biology Founding Education Editor, announced the launch of a new Education column in the journal. This new column recognised the need for bioinformatics and computational biology training and education specifically targeted to biologists. Since then, the Education section has proven to be an extremely valuable resource for the community, with over 50 articles published within the Education collection itself and a further two collections launched under its banner, Bioinformatics: Starting Early and Translational Bioinformatics.

After eight years as Education Editor, we’re sad to announce that Fran Lewitter is now stepping down from this position. She will, however, be remaining with the journal as an Editorial Advisory Board member. To mark the end of her time in the role of Education Editor, she reflects on the journey she has taken and offers some words of wisdom on the power of networking in her new Editorial, Moving Education Forward, Again! None of the achievements mentioned above would have been possible without Fran’s hard work and dedication, and we are extremely grateful for all her support. Phil Bourne, Founding Editor-in-Chief of PLOS Computational Biology comments on Fran’s accomplishments:

Image Credit: PLOS


“Fran has been a wonderful asset to the journal and is largely responsible for making the Education Section of PLOS Computational Biology such a success over the years. I enjoyed working with her immensely. Our community should recognise her dedication and commitment to teaching.”



This is, however, not the end of the ever-popular PLOS Computational Biology Education section! We are delighted to announce that Francis Ouellette and Joanne Fox will be joining the PLOS Computational Biology Editorial Board as our new Education Editors.  Francis and Joanne have both been involved in a variety of education initiatives, both within their institutions (Ontario Institute for Cancer Research and the University of British Columbia) and in their community outreach efforts, and we look forward to the insights they can bring to the Education section. To find out more about the new Editors and their plans for the section, take a look at their first Editorial, “Education in Computational Biology Today and Tomorrow”.

We can’t wait to see what the next eight years will bring!

You can visit the Education collection at:

Category: Announcement, Community, Computational biology, Education, News, Outreach, PLOS Computational Biology | Tagged , | Leave a comment

And Another Thing: Supporting Information Files at PLOS

Today PLOS announced a revised Data Policy that will come into effect on 1 March 2014, bringing in further measures to ensure that access to the data underlying research is an intrinsic part of the scientific publishing process. In that policy, the most strongly recommended data-sharing method is data deposition in an appropriate public repository. However, especially for smaller datasets and certain data types, the use of supporting information – those accompanying, peripheral files that are attached to a published article – may be appropriate. So, while we contemplated data policy, we at PLOS have also been thinking about supporting information: what we use it for, where it is helpful, where it isn’t, and how to approach it in an online, open data world. And we’d like to seek your thoughts too – so read on.

Supporting information can be useful

The accompaniment of research articles with supporting information is a relatively new development in scientific publishing, made possible with online formats. And the first thing we’d like to acknowledge is that it can be useful: it has opened new possibilities for research communication.

For example, researchers may:

  • make the raw underlying data available for further work or replication;
  • supply extra detail on methods;
  • add figures or tables that are related to the study but not central;
  • add multimedia or other file types that can’t yet be incorporated directly into the article;
  • provide information to make their study more accessible (such as a translation into another language).

Journals also make specific uses of supporting files: for example, they may request that authors include documents showing adherence to field-specific guidelines such as ARRIVE or CONSORT, or provide the study protocol.

But it also creates challenges

As articles include more and more supporting information, we ask ourselves, and you:

  • In practice, do peer reviewers assess supporting information sufficiently as part of their review? If not, some important information may not be reviewed; and perhaps some supporting information files require more review than others.
  • Which information associated with the article should the journal host, and which information should be hosted elsewhere? It is worth considering: how immediately accessible the information will be from the article; the permanence of storage at either location; and how both human and machine readers would go about searching for, and within, the supporting information.
  • If the use of supporting information has been shaped primarily by authors and journals, how has this affected readers? Do they miss information that could be important to the main study when it is in the supporting information? Is the distribution of information between the main article and supporting information determined by factors we can overcome in the online world, such as article length restrictions? Or would addition of some supporting information content to the main article impede comprehension?

Some recommendations

We would like to make the case that while supporting information definitely has a role in research communication, there are ways of using it more responsibly – thereby improving the quality, coherence and completeness of published work. We recommend the following two approaches to responsible use of supporting information:

  • Ask: does it need to be a supporting information file? Before making a supporting information file, consider incorporating the information into the main manuscript or (if it contains data) sending it to an appropriate public repository. The main manuscript is more immediately accessible and searchable by readers, editors, and reviewers than is supporting information; and established public repositories can optimize for the storage and retrieval of datasets.
  • Consider machine-readability and reusability. Files can be made as usable as possible to reviewers, readers, and computational ‘readers’ by selecting a format from which data can be extracted: for example a spreadsheet rather than a PDF.


It doesn’t end here

We hope that by raising this topic with you – our authors, readers, reviewers, editors, and others – we can start to consider together the most helpful role for supporting information in research communication. Within PLOS, we’ll be continuing to develop our understanding of how supporting information is currently used, how we can best work with authors to optimize its use, and what technological solutions we could pursue to complement responsible supporting information file use. As we do this, we also want to know: what would your recommendations be? We invite you to comment here on the blog, via or contacting the individual journals directly; we’ll also monitor Twitter and other sources.


Rosalind Attenborough, Publications Manager, PLOS Genetics

for the PLOS Supporting Information Files group

Category: Data, Policy | 2 Comments

PLOS Biology at ASCB 2013: Open for Cell Biology

ASCB meet editorsAt PLOS Biology, we strongly believe that we are open for a reason: our aim is to publish high quality research in areas of broad significance, ensuring that it reaches the widest possible audience without any barriers to access. Cell biology is an area of research that we believe should be as openly available as possible by being published in an open access, CC-BY journal, with associated data being mineable and reusable.

PLOS Biology publishes cell biology research of exceptional significance, originality, and relevance that informs research in its field and influences thinking beyond. We encourage you to consider PLOS Biology as a high visibility outlet for your future research. We are interested in all areas of cell biology. To get a taste of the research in cell biology that we have recently published, check out the links below to access the latest research in this field.

I will be attending the 2013 American Society of Cell Biology annual meeting in New Orleans next week together with my colleagues from PLOS ONE, and while there I very much look forward to meeting with our Academic Editors, authors, and reviewers in the cell biology research community.

If you are also attending the meeting and would like to find out more about how to publish in an Open Access journal, please visit us at the PLOS booth, number 211, where you can meet me and my PLOS colleagues. PLOS Biology is organizing a ‘meet the editor’ session on Monday, December 16, from 12-1pm – so do come by then. Alternatively, you can email me at plosbiology[at] to arrange a time to chat.

Looking forward to meeting you in New Orleans!


OA logo



If you are interested in cell biology, you might want to read the following research articles – all Open Access and available to read to all:


The Circadian Clock Coordinates Ribosome Biogenesis. Céline Jouffe, Gaspard Cretenet, Laura Symul, Eva Martin, Florian Atger, et al. (2013)


Molecular Remodeling of Tip Links Underlies Mechanosensory Regeneration in Auditory Hair Cells. Artur Indzhykulian, Ruben Stepanyan, Anastasila Nelina, Kateri Spinelli, Zubair Ahmed, et al. (2013)


A Meiosis-Specific Form of the APC/C Promotes the Oocyte-to-Embryo Transition by Decreasing Levels of the Polo Kinase Inhibitor Matrimony. Zachary Whitfield, Jennifer Chisholm, R. Scott Hawley, Terry Orr-Weaver (2013)


Dynactin Subunit p150pGlued Is a Neuron-Specific Anti-Catastrophe Factor. Jacob Lazarus, Armen Moughamian, Mariko Tokito, Erika Holzbaur (2013)


Partial Inhibition of Adipose Tissue Lipolysis Improves Glucose Metabolism and Insulin Sensitivity Without Alteration of Fat Mass. Amandine Girousse, Geneviève Tavernier, Carine Valle, Cedric Moro, Niklas Mejhert, et al. (2013)


Strigolactone Can Promote or Inhibit Shoot Branching by Triggering Rapid Depletion of the Auxin Efflux Protein PIN1 from the Plasma Membrane. Naoki Shinohara, Catherine Taylor, Ottoline Leyser (2013)


Molecular Composition and Ultrastructure of the Caveolar Coat Complex. Alexander Ludwig, Gillian Howard, Carolina Mendoza-Topaz, Thomas Deerinck, et al. (2013)


HDAC4 Reduction: A Novel Therapeutic Strategy to Target Cytoplasmic Huntingtin and Ameliorate Neurodegeneration. Michal Mielcarek, Christian Landles, Andreas Weiss, Amyaouch Bradaia, et al. (2013)


Anthranilate Fluorescence Marks a Calcium-Propagated Necrotic Wave That Promotes Organismal Death in C. elegans. Cassandra Coburn, Erik Allman, Parag Mahanti, Alexandre Benedetto, et al. (2013)


Front Matter

No Question about Exciting Questions in Cell Biology. Tom Pollard (2013).


Deducing Protein Function By Forensic Integrative Cell Biology. Bill Earnshaw (2013). In press.


Category: Announcement, Cell biology, Conference, Open access, PLOS Biology | 1 Comment

Holiday reading with PLOS Genetics

Do you have a reading list this holiday season? Unsure what to buy for your lab’s Secret Santa this year? Here at PLOS Genetics our usual business is strictly scientific, but we’re also interested in how science and genetics meet a wider community – and one of those ways is through literature (not just of the research variety!).

To celebrate our broader horizons as scientists and science enthusiasts (as well as our simple desire for a good book), PLOS Genetics has just launched Deep Reads, a new article series inspired by our interviews editor, Jane Gitschier, who has run a genetics-themed book club for the past 10 years or so. Jane has written the first instalment, Recommendations from Jane Gitschier’s Bookshelf, but hopes that other members of the genetics community will subsequently take up the pen.

Image credit: State Library of New South Wales (Flickr)

Image credit: State Library of New South Wales (Flickr)

The article is a catalogue of her favourite books related to science, stepping off from genetics but going beyond into other scientific domains. Many of our readers will already know and love Jane’s collection of interviews, in which she talks to influential people from the world of genetics about their scientific discoveries and life stories. In a similar conversational style, Jane takes us through a journey of memoirs and biographies, and delves into a variety of non-fiction and fiction. We’re delighted that she has provided the initiative to kick-off the new Deep Reads series, and we look forward to reading others’ top literary picks in future instalments.

As a community journal, PLOS Genetics is run by and for scientists, whether full-time researchers, students, or those with an interest in genetics and genomics. With the launch of Deep Reads, we hope to learn about the books that you’ve read and your views on science in literature. Have they affected your perception of science?  How do you think reading about the lives of scientists in the past has influenced the lives of researchers today? Perhaps there was a book that spurred you on to investigate a certain aspect of genetics, or motivated you as you began your career in science. If you’re looking for some holiday reading or deciding on gifts for your family and friends, we hope that this list of books also provides some inspiration as the holiday season approaches!

If you have read any of the books recommended by Jane or have some of your own “Deep Reads” to recommend, we invite you to tell us by leaving a comment here, tweeting @PLOSGenetics (#PLOSGenReads), or emailing us at

Category: Announcement, Biology, Blog, Books, Community, Genetics, PLOS Genetics | Tagged , , , | Leave a comment

Reconstructing gene regulatory networks, dreading future pain and the About My Lab collection: the PLOS Comp Biol November issue

Here is our selection PLOS Computational Biology highlights for November.

PLOS Comp Biol Featured Image for November. Image Credit: Guido Polles

PLOS Comp Biol Featured Image for November. Image Credit: Guido Polles

The study of gene regulatory networks is essential to understanding how diseases function at a system level. Hiroaki Kitano and colleagues developed an algorithm called TopkNet that can integrate multiple algorithms in order to infer gene regulatory networks. The authors aim to provide a method to reconstruct high quality versions of these networks and thereby gain greater knowledge for successful reverse engineering on biomedical research.

A paper that received some notable press attention this month is “Dread and the Disvalue of Future Pain”. The paper, by Giles Story et al., shows that the expectation of future pain creates dread, which increases the more the pain is delayed. However, as pain moves further into the future, the effect of delay decreases.

November also saw the launch of our new collection, About My Lab. The collection, edited by Theodore Alexandrov and Philip E. Bourne, aims to share insights into the running of a lab. Each article is written from the perspective of a Principal Investigator in their own personal style. In publishing this collection we hope to further the dialogue between old, young and future PIs.

By Chris Hall, Senior Publications Assistant, PLOS Computational Biology

Category: Biology, Community, Genetics, Neuroscience, PLOS Computational Biology | Tagged , | Leave a comment