Back to back viral fun in the UK! 8th Aquatic Virus Workshop (AVW8) from 10 – 13 July 2016, in Plymouth UK (save the date) and Viruses of Microbes meeting

The Gordon and Betty Moore Foundation’s Marine Microbiology Initiative is investing eight million dollars over the next two years to support scientists, globally and at all career stages, to accelerate development of experimental model systems in marine microbial ecology. The researchers have been encouraged to use Protocols.io to release novel protocols for studying marine microbes. The Protocols.io team has been collaborating with Bonnie Hurwitz of the University of Arizona (UA)’s BIO5 Institute on VERVE Net, the Viral Ecology Research and Virtual Exchange Network created by Hurwitz to enable protocol sharing within the viral ecologist community. In addition, Hurwitz is the creator of the iMicrobe project that provides data and Apps for microbial research. Both iMicrobe and VERVE Net are funded by the Gordon and Betty Moore Foundation. Data for iMicrobe is hosted by the iPlant Collaborative, a data management platform for the life sciences headquarted at the UA. The international endeavor taps into the efforts of more than 100 scientists across 33 institutions with a broad range of expertise to collectively tackle the challenge of developing methods to bring experimental model systems to the ocean. The genetic tools generated in this effort will allow researchers to more easily disrupt the activities of microbial genes to understand how these organisms function in marine ecosystems and provide the capability to ask scientific questions in ways not currently possible.

I have been asked countless times by students, “where can I find the most up to date bioinformatics protocols” and sadly my response has always been “by trolling through the literature and trying to find a paper with analyses that are similar to what you propose to do”. Even then, replicating the methods in these papers can be difficult given the numerous “custom perl scripts” and shell commands only know to the authors. Hey! It is even hard to reproduce my own work. Times are changing! Bioinformatics Protocols can now be documented and released to the community for re-use at Protocols.io (akin to Github). This work has been done through the VERVENet project (Hurwitz Lab) in collaboration with the team at Protocols.io.

The Hurwitz lab and the iMicrobe project are collaborating with Larry Peterson of UA computer science; Nirav Merchant of the iPlant Collaborative and Arizona Research Laboratories; John Hartman of UA computer science; and Anita Bapphu of the Norton School of Family and Consumer Sciences on the OpenCloud project Syndicate. Syndicate is a global-scale distributed file system being developed on XOS and deployed on OpenCloud. The Syndicate project is working closely with iPlant to enable iPlant researchers around the world to access access datasets efficiently and easily via Syndicate, and has recently received an NSF research grant in support of this effort.

Now that we have ironed out most of the bugs through the VERVE Net, we are opening up the group functionality in protocols.io. This means that you can create your own group (for a lab or class) and enter protocols associated with that group.  You can reach groups through the regular protocols.io site here.  You will then click on the ‘explore’ button and go into ‘browse groups.’  You can create a group by clicking the “+ groups” sign next to your picture in the upper left hand corner of protocols.io. *Be sure to create a login first.

You can also join the viral ecology group: VERVE Net.  Click on the ‘join group’ button on the VERVE Net group page.  

Check out the recent UA news article on our VERVE Net grant.  Also, our first implementation of VERVE Net is up and running check it out.    

Check out our new publication on The Quest for Tissue Repair’s Holy grail: the Promise of Wound Diagnostics or just another Fishing Expedition.

Great News for the Viral Ecology Community!  We were just funded by the Gordon Betty Moore Foundation to deliver VERVE Net:

VERVE Net: Viral Ecology Research and Virtual Exchange Network

Bonnie Hurwitz, PhD, PI, University of Arizona; Lenny Teytelman, PhD, Scientific Lead, ZappyLab

The advent of metagenomic methods to sequence DNA directly from an environment has revolutionized viral ecology, making it possible to “see” natural viral communities that could not be previously studied through culture.  This technological leap has enabled further innovation in: extracting and sequencing limited viral DNA from communities, enriching and sequencing wild viruses through single-cell genomics, and creating new bioinformatics methods for large-scale comparative and functional metagenomics.  Yet, the knowledge for specialized techniques in viral ecology remains in a subset of labs.  We are developing a viral ecology community forum called VERVE Net to increase connectivity and knowledge dissemination in viral ecology research at all levels from undergraduates to accomplished viral ecologists.  VERVE Net will leverage and refine existing software from ZappyLab to enhance a researcher’s ability to: discuss and share protocols (via protocols.io), connect with fellow community members (VERVE Net community forum), and learn about new and innovative research in the field (via PubChase).  In delivering these valuable tools, VERVE Net will become a central resource to connect, collaborate, share and innovate for the viral ecology community. 

Greetings from Spain and the American Society for Limnology and Oceanography conference!  Check out the latest and greatest for the iMicrobe Project to: Promote reuse and discovery of large-scale  –omics datasets through a common ecosystem of tools, data storage, and computational resources by re-purposing the iPlant Cyberinfrastructure. Slides are Here.

Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’

http://www.biomedcentral.com/1741-7015/13/2