PLOS ONE Launches Synthetic Biology Collection

Today PLOS ONE is happy to announce the launch of the Synthetic Biology Collection, including over 50 papers published in the last six years that illustrate the many facets of this dynamically evolving research area.

Synthetic biology is an innovative emerging field that exists at the intersection of many traditional disciplines, including biology, chemistry, and engineering, with aims to create biological systems that can be programmed to do useful things like produce drugs or biofuels, among other applications. Despite its potential, the heavily interdisciplinary nature of the research can make it difficult to publish in traditional discipline-specific journals.

However, PLOS ONE’s broad scope allows for the publication of work crossing many traditional research boundaries, making it an ideal venue for many different types of synthetic biology research. For example, the papers in the collection cover topics including DNA synthesis and assembly, standardized biological “parts” akin to interchangeable mechanical parts, protein engineering, and complex network and pathway analysis and modeling, as described in the Collection Overview written by collection editors Jean Peccoud of Virginia Tech and Mark Isalan of the Centre for Genomic Regulation.

The Collection has roots in PLOS ONE’s very first issue, which included two publications from the field. Since then, the number of synthetic biology articles published in the journal has grown steadily. The collection launched today highlights selected synthetic biology articles published in PLOS ONE since 2006, and it is intended to be a growing resource that will be updated regularly with new papers as the field continues to grow and develop.

Collection Citation: Synthetic Biology (2012) PLOS Collections: http://www.ploscollections.org/syntheticbiology

Image Credit: Ivan Morozov (Virginia Bioinformatics Institute)


PLOS ONE Launches Reproducibility Initiative

PLOS ONE is pleased to announce a collaboration with Science Exchange and figshare in a groundbreaking new project: The Reproducibility Initiative. The initiative aims to help scientists validate their research findings by providing a mechanism for blind, independent replication by experts from Science Exchange’s network of more than 1,000 providers at core facilities and contract research organizations.

Reproducibility, or the lack thereof, is a known issue in the scientific community, but few have the time or resources to fully address it. The Reproducibility Initiative is intended to encourage authors to validate their work by facilitating collaboration with an unbiased expert, and offering a Certificate of Reproducibility upon completion. This project will benefit stakeholders from across the research spectrum, including research scientists, drug companies, publishers, funders, and patient groups, all of whom agree that independent confirmation of results improves science and speeds discovery.

When PLOS ONE launched in 2006, a key objective was to publish those findings that historically did not make it into print: the negative results, the replication studies, the reanalyses of existing datasets. Although everyone knew these studies had value, journals would rarely publish them because they were not seen to be sufficiently important. PLOS ONE sought to become a venue for exactly these types of studies. As it happened, however, the submissions were not hugely forthcoming, although we have published a few. (One paper, for example, replicated a previous MRI study but used a higher resolution to confirm the findings, while another failed to replicate a famous psychology study from the nineties.) The Reproducibility Initiative harks back to this original objective, and may even open the doors to more papers whose sole purpose is to correct the literature.

The initiative brings together a number of scientific innovations to create a completely new research space. Science Exchange enables experiments to be performed objectively, free of the pressure to produce positive results that affects most scientists; PLOS ONE provides a formal publication venue that will publish the results of replication studies, even though they are not ‘novel’; and figshare provides a means of sharing raw data quickly and efficiently.

The Reproducibility Initiative is initially accepting 40-50 studies for validation. Scientists can submit their studies here. They will be selected on the basis of potential clinical impact and the scope of the experiments required. The organizers of the project hope that it will be the start of a more overarching system of validation by funders and patient groups, and that’s a sentiment we at PLOS ONE would certainly be happy to see replicated.

PLoS ONE launches the NeuroMapping & Therapeutics Collection

The following blog is by Babak Kateb, curator of the PLoS ONE NeuroMapping & Therapeutics Collection

One of the great challenges of the 21st century is how to translate scientific advancements from physical sciences into medicine. This gap of knowledge is also clearly visible amongst multiple disciplines within medicine (i.e. neurosurgery and radiology, neurology and neurosurgery, psychiatry and radiology and radiology and neurology). In this spirit, the Society for Brain Mapping and Therapeutics (SBMT) has been successfully addressing this educational gap by bringing together physicians, surgeons, scientists and engineers from multiple disciplines to promote cross-disciplinary research and publication.

To foster increased dialogue between these communities, PLoS ONE has launched a special collection entitled SBMT NeuroMapping & Therapeutics. The SBMT encourages its members to publish their research in PLoS ONE. These articles will then be brought together into an ongoing Collection that will highlight this content.

The aim of the SBMT NeuroMapping & Therapeutics Collection is to provide a forum for interdisciplinary research aimed at translation of knowledge across a number of fields such as:

  • Neurosurgery (e.g. Image Guided Therapy/intervention, brain tumors and intraoperative navigation, nanoneurosurgery, stereotactic radiosurgery, minimally invasive therapy, vascular neurosurgery, functional neurosurgery…)
  • Neurology (e.g. movement disorders, neurodegenerative diseases, neurooncology, as well as image guided device implantation…)
  • Psychiatry (e.g. medical imaging for psychiatric conditions such as schizophrenia, depression, PTSD…)
  • Radiology (e.g. fMRI, PET, Nuclear medicine, MR SPEC, MRI, MR-PET, DTI, CT-PET, Focused Ultrasound, SQUID MRI, low magnet MRI…)
  • Neuroscience (e.g. stem cell, molecular neuroscience, image guided mapping of genes, proteomics, genomics…)
  • Neuroengineering (e.g. iomaterial & tissue engineering, human brain Machine Interface, brain and spinal cord devices, nanomedicine, extraterrestrial/space medicine & clinical practice…)
  • Policy (e.g. healthcare policy issues that affect the treatment delivery and usage of certain devices/drugs/imaging technologies…)

This Collection will contain a selection of those articles published within PLoS ONE, which the Editorial Board of the Collection feel are representative of the aims and scope of the SBMT society.  It will continue to expand over time as the number of relevant articles grows and are added to the Collection.

The SBMT welcomes submissions to the PLoS ONE NeuroMapping & Therapeutics Collection. If you wish to submit your research please consider the following when preparing your manuscript:

  • Submission to PLoS ONE as part of the NMT Collection does not guarantee publication or inclusion into the final Collection due to highly competitive nature of this collection.

When you are ready to submit your manuscript to the collection, please log in to the PLoS ONE manuscript submission system and select the ‘SBMT NeuroMapping & Therapeutics Collection’ from the dropdown menu to ensure the PLoS ONE staff are aware of your submission.

Please contact Sam Moore (smoore@plos.org) if you would like further information about how to submit your research to the PLoS ONE NeuroMapping & Therapeutics Collection.

The following PLoS ONE Editorial Board members have agreed to assist with this collection:

  • Dr. Krystof Bankiewicz, University of California at San Francisco, US
  • Dr. Mitch Berger, University of California at San Francisco, US
  • Dr. Keith Black, Cedars-Sinai Medical Center, US
  • Dr. Aria Tzika, Harvard Medical School and Massachusetts General Hospital, US
  • Dr. Michael Lim, Johns Hopkins Hospital, US
  • Dr. Antoni Rodriguez-Fornells, University of Barcelona, Spain
  • Dr. Shawn Hochman, Emory University, US
  • Dr. Stephen Ginsberg, Nathan Kline Institute and New York University School of Medicine, US
  • Dr. Andreas Meisel, Charité Universitaetsmedizin Berlin, Germany
  • Dr. Hitoshi Okazawa, Tokyo Medical and Dental University, Japan
  • Dr. Joseph El Khoury, Massachusetts General Hospital and Harvard Medical School, US
  • Dr. Karin Peterson, National Institute of Allergy and Infectious Diseases – Rocky Mountain Laboratories, US
  • Dr. Tsuneya Ikezu, Boston University School of Medicine, US
  • Dr. Mike Chen, City of Hope, US
  • Dr. Christopher Wheeler, Cedars-Sinai Medical Center, US
  • Dr. Maya Koronyo-Hamaoui, Cedars-Sinai Medical Center, US
  • Dr. Alfredo Quinones-Hinojosa, Johns Hopkins Hospital, US

 

Curators: Babak Kateb and Allyson C. Rosen

Announcing the Human Microbiome Project Collection

For the first time, a consortium of researchers has mapped the full community of microbes that inhabit various parts of the healthy human body. Many of these findings will be published today in a new PLoS collection. The PLoS Human Microbiome Project Collection consists of articles from the project’s consortium members, who generate, leverage, and explore microbiome analytical techniques. The articles have been culled from PLoS ONE, PLoS Genetics, and PLoS Computational Biology with more being added to the collection as they are published.

The manuscripts within the collection provide a comprehensive baseline of the microbial diversity at 18 different human body sites. This baseline includes reference genomes of thousands of host-associated microbial isolates, 3.5 terabases of metagenomic sequences, assemblies, and metabolic reconstructions, and a catalogue of over 5 million microbial genes.

Some of the studies also look at the relationships between the microbiome and the host, and how these interactions relate to health. They describe how specific microbial communities differ in relation to a number of specific conditions: the gut microbiome and  Crohn’s disease; ulcerative colitis and esophageal adenocarcinoma; the skin microbiome and psoriasis, and atopic dermatitis and immunodeficiency; and urogenital microbiome and reproductive and sexual history and circumcision and a number of childhood disorders, including pediatric abdominal pain and intestinal inflammation, and neonatal necrotizing enterocolitis.

Accompanying this collection are two articles published in the journal Nature by the Human Microbiome Project Consortium. The results of these two papers provide the foundation for the research published in the Human Microbiome Project Collection.

To read more about this collection, please visit:

PLoS Collections: The Human Microbiome Project Collection (2012) www.ploscollections.org/hmp

PLoS ONE Launches the Mice Drawer System Experiment Collection

In August 2009, the Italian Space Agency launched its Mice Drawer System (MDS) investigation on the Shuttle Discovery flight 17A/STS-128. Over the course of a 91-day mission at the International Space Station, the MDS experiment focused on the effects of microgravity on six mice. The purpose of the experiment was to investigate the structural and functional changes that occur in animals when there is an absence of normal gravity over an extended period of time.

The new PLoS ONE Collection brings together a number of articles drawn from this long-term project.

The research presented attempts to capture information on a range of mammalian physiological system changes during the space flight. Collectively the articles offer an integrative view of the mammal’s physiological response to a microgravitational climate.

The research was an international collaboration and involved scientists from several countries. With a better understanding of the effect of microgravitational conditions on mice, this research could be applied in ways to help extend the human presence in space beyond low Earth orbit.

Adapted from: Cancedda R, Liu Y, Ruggiu A, Tavella S, Biticchi R, et al. (2012) The Mice Drawer System (MDS) Experiment and the Space Endurance Record-Breaking Mice. PLoS ONE 7(5): e32243. doi:10.1371/journal.pone.0032243

Collection Citation: The Mice Drawer System Experiment and the Space Endurance Record-Breaking Mice (2012) PLoS Collections: http://www.ploscollections.org/Mice_Drawer_System

Voluntary Medical Male Circumcision (VMMC) – a cost-effective HIV prevention measure in eastern and southern Africa: a UNAIDS and PEPFAR collection

Editor’s note: Earlier this week, PLoS Medicine announced the publication of a sponsored Collection, in conjunction with the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the United States President’s Emergency Plan for AIDS Relief (PEPFAR) –  Voluntary Medical Male Circumcision for HIV Prevention: The Cost, Impact, and Challenges of Accelerated Scale-Up in Southern and Eastern Africa. In addition to containing research articles and reviews from PLoS Medicine, this Collection also contains a few PLoS ONE manuscripts.  The following post explains this Collection and was originally posted on PLoS Medicine’s blog, Speaking of Medicine. It was written by Sumrina Yousufzai, a Publications Manager who works for PLoS Medicine.

The Collection comprises four reviews and five research articles, and highlights how scaling up voluntary medical male circumcision (VMMC) for HIV prevention in eastern and southern Africa can help prevent HIV, not only at the individual level but also at the community and population level, as well as leading to substantial cost savings for countries due to averted treatment and care costs. Two of the research articles are published in PLoS ONE; the remaining seven articles are published in PLoS Medicine on 29th November 2011. They can be accessed from the PLoS Medicine VMMC Collection page; the table of contents is also included below.

The first article by Catherine Hankins of UNAIDS, Steven Forsythe of The Futures Institute, and Emmanuel Njeuhmeli of PEPFAR/USAID, offers an introduction to the cost, impact and challenges of accelerated scaling up and lays out the rationale for the Collection. The remaining eight papers focus on the various factors that have important roles in effective program expansion of VMMC, including data for decision making, policy and programmatic frameworks, logistics, demand creation, human resources, and translating research into services.

The potential cost savings of scale-up are clear. An initial investment of US$1.5 billion between 2011 and 2015 to achieve 80% coverage of VMMC services in 14 priority countries in southern and eastern Africa, and thereafter US$0.5 billion between 2016 and 2025 to maintain coverage of 80%, could result in net savings of US$16.5 billion between 2011 and 2025. However, as the articles in the Collection show, strong political leadership, country ownership, and stakeholder engagement, along with effective demand creation, community mobilization and human resource deployment, are essential for effectively expanding and maintaining VMMC programs.

All 9 articles were peer-reviewed, revised and considered in depth by the editorial team, and subjected to all the usual PLoS Medicine or PLoS ONE editorial processes. We would like to thank the numerous peer reviewers for their detailed critiques, which helped to shape the articles, and we would also like to thank the authors for their patience in making appropriate revisions to these reviews. In particular we would like to Stephanie Sansom, guest academic editor, who read all the articles and provided critical feedback and reviewer advice to the editorial team. A special thank you goes to Emmanuel Njeuhmeli of PEPFAR/USAID who served as the main editorial contact for the articles in this Collection.

A question-and-answer Twitter expert session [#VMMC@USAIDGH] will be held on December 19 2011, from 1pm-2pm EST, with Emmanuel Njeuhmeli, Senior Biomedical Prevention Advisor of the Office of HIV/AIDS/USAID Washington, Co-Chair PEPFAR, Male Circumcision Technical Working Group, and an author on several of the articles in the Collection. In regard to this Collection Dr. Njeuhmeli comments:

“The collaboration that led to the findings in the PLoS Collection is a true testament to what international partners can accomplish when they work together and do so effectively to support country strategy for HIV Prevention. I can say with confidence this collaboration has played a major role in moving the needle on VMMC and HIV prevention. This Collection represents extensive collaboration between Ministries of Health, WHO, UNAIDS, PEPFAR and implementing partners to document and share with policy makers and program implementers the estimated cost and potential impact of scaling up voluntary medical male circumcision (VMMC) services in southern and eastern Africa. The papers included in this Collection document the enormous potential of VMMC to alter the course of the epidemic. They also describe the way that country programs have successfully navigated human resource, demand generation and other challenges in an effort to rapidly scale up comprehensive VMMC services.”

Collection Table of Contents :

1)     Voluntary Medical Male Circumcision: An Introduction to the Cost, Impact, and Challenges of Accelerated Scaling Up

2)     Voluntary Medical Male Circumcision: Modeling the Impact and Cost of Expanding Male Circumcision for HIV Prevention in Eastern and Southern Africa

3)     Voluntary Medical Male Circumcision: A Framework Analysis of Policy and Program Implementation in Eastern and Southern Africa

4)     Voluntary Medical Male Circumcision: A Cross-Sectional Study Comparing Circumcision Self-Report and Physical Examination Findings in Lesotho

5)     Voluntary Medical Male Circumcision: Logistics, Commodities, and Waste Management Requirements for Scale-Up of Services

6)     Voluntary Medical Male Circumcision: A Qualitative Study Exploring the Challenges of Costing Demand Creation in Eastern and Southern Africa

7)     Voluntary Medical Male Circumcision: Strategies for Meeting the Human Resource Needs of Scale-Up in Southern and Eastern Africa

8)     Voluntary Medical Male Circumcision: Translating Research into the Rapid Expansion of Services in Kenya, 2008–2011

9)      Voluntary Medical Male Circumcision: Matching Demand and Supply with Quality and Efficiency in a High-Volume Campaign in Iringa Region, Tanzania

Disclaimer: The views expressed in the VMMC collection are those of the authors and do not necessarily reflect the official policy or position of the U.S. Government and UNAIDS. The collection was produced with support from the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the United States President’s Emergency Plan for AIDS Relief (PEPFAR). The PLoS Medicine editors have sole editorial responsibility for the content of this collection.

Image Credit: PEPFAR Male Circumcision Technical Working Group

Permission to use the CCAL license granted by the PEPFAR Male Circumcision Technical Working Group.

Altmetrics: Tracking scholarly impact on the social Web – PLoS ONE Collection

The huge increase in scientific output is presenting scholars with a deluge of data.  There is growing concern that scholarly output may be swamping traditional mechanisms for both pre-publication filtering (e.g. peer review) and post-publication impact filtering (e.g. the Journal Impact Factor).

Increasing scholarly use of Web 2.0 tools like CiteULike, Mendeley, Twitter, and blogs presents an opportunity to create new filters.  Metrics based on a diverse set of social sources could yield broader, richer, and timelier assessments of current and potential scholarly impact.  Realizing this, many authors have begun to call for investigation of these metrics under the banner of “altmetrics.”  Specifically, altmetrics is the creation and study of new metrics based on the Social Web for analyzing and informing scholarship.

Despite the growing speculation and early exploratory investigation into the value of altmetrics, there remains little concrete, objective research into the properties of these metrics: their validity, their potential value and flaws, and their relationship to established measures. Nor has there been any large umbrella to bring these multiple approaches together.

Following on from a first successful workshop on altmetrics, this collection aims to provide a forum for the dissemination of innovative research on these metrics.

We seek high quality submissions that advance the understanding of the efficacy of altmetrics, addressing research areas including:

  • Validated new metrics based on social media.
  • Tracking science communication on the Web.
  • Relation between traditional metrics and altmetrics including validation and correlation.
  • The relationship between peer review and altmetrics.
  • Evaluated tools for gathering, analyzing, or disseminating altmetrics.

Papers will be reviewed on a rolling basis in-line with PLoS ONE standard practices.

Please note that all submissions submitted before January 28th, 2012 will be considered for the launch of the collection (expected spring 2012); submissions after this date will still be considered for the collection, but may not appear in the collection at launch.

Submission Guidelines

If you wish to submit your research to the Altmetrics: Tracking scholarly impact on the social Web Collection, please consider the following when preparing your manuscript:

– All articles must adhere to the PLoS ONE submission guidelines.

– Standard PLoS ONE policies and publication fees apply to all submissions.

– Submission to PLoS ONE as part of the Altmetrics Collection does not guarantee publication.

When you are ready to submit your manuscript to the collection, please log in to the PLoS ONE manuscript submission system and insert ‘Altmetrics’ in the relevant field to ensure the PLoS ONE staff are aware of your submission to the Collection.  Once you have registered, you can follow the steps for manuscript submission.

Please contact Lindsay King (lking@plos.org) if you would like further information about how to submit your research to the PLoS ONE Altmetrics Collection.

Organizers:

Paul Groth, VU University Amsterdam

Dario Taraborelli, Wikimedia Foundation

Jason Priem, UNC-Chapel Hill

About PLoS ONE

PLoS ONE (eISSN-1932-6203) is an international, peer-reviewed, openaccess, online publication.  PLoS ONE welcomes reports on primary research from any scientific discipline.

It provides:

  • Open-access – freely accessible online, authors retain copyright
  • Fast publication times
  • Peer review by expert, practicing researchers
  • Post-publication tools to indicate quality and impact
  • Community-based dialogue on articles
  • Worldwide media coverage
  • PLoS ONE is published by the Public Library of Science (PLoS), a nonprofit organization.

PLoS ONE Launches the RosettaCon 2010 Collection

Reproducing computational biology protocols is one of the difficult challenges facing computational biologists today. Often times, it is rarely feasible to replicate the computational environment of an original work because of the complexity of macromolecular modeling protocols.  Moreover,  much of this work is new research and not focused solely on the algorithms or workflows.  As a result, published results often contain method descriptions with inconsistently stated protocols and dependencies.

In the new PLoS ONE Collection: RosettaCon 2010, over 15 academic groups from Rosetta Commons have attempted to capture these protocols in a sufficiently complete and formal way. This Collection aims to make several of the latest Rosetta macromolecular modeling protocols from the 2010 Rosetta Developers Meeting accessible to all.

Three main contributions came from the meeting and are represented in the PLoS ONE Collection.

1. New Rosetta applications: Several articles describe specific applications in biology or chemistry, including de novo enzyme design, modeling classes of protein loops, design of temperature sensitive mutations, and design of peptides to inhibit large surface area protein interactions.

2. Rosetta basic science: Several of the contributions in this Collection are Rosetta basic science papers of this type.  Examples include: incorporation of non-canonical amino acids in Rosetta design, multi-state design, new Rosetta kinematics, new protein docking protocols, and anchored design. Each example has the full protocol that lead to the incorrect prediction fully described as well as the correct (“native”) structure; thus these protocols are key elements in defining and judging future improvement in Rosetta and other codes.

3. Rosetta code development: Multiple articles describe new code refactoring, extensions or improvements to the implementation of Rosetta.  Several articles discuss the creation of multi-purpose high level interfaces to the components of Rosetta.  Examples include an XML scripting interface for Rosetta, an interactive python interface to the Rosetta code, and an object oriented API for generating Rosetta fragments.

RosettaCon 2010 provides the larger community direct access to the exact protocols used in each of these papers. This construction was intended to allow other community members and Rosetta users to reproduce the work, allow competing groups to validate and improve upon the work, and finally, make it rapidly accessible to new users with similar biological applications.

It should be noted that this Collection is itself a social experiment and the collaborators wrestled with how best to capture an evolving set of processes in a way that does not overly burden authors, works across a distributed community without a central authority for methods capture, is timely, and is sufficiently self-consistent that readers will invest their time in the results.

The paper, 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing, by Renfrew et al. was adapted to create this post.

Collection Citation: RosettaCon 2010 (2011) PLoS Collections: http://www.ploscollections.org/RosettaCon2010