Author Archives: Bonnie Hurwitz

New Pub: Virtual Communities for Protocols Development and Discussion

Virtual Communities for Protocols Development The detailed know-how to implement research protocols frequently remains restricted to the research group that developed the method or technology. This knowledge often exists at a level that is too detailed for inclusion in the methods section of scientific articles. Consequently, methods are not easily reproduced, leading to a loss of time and effort by other researchers. The challenge is to develop a method-centered collaborative platform to connect with fellow researchers and discover state-of-the-art knowledge. is an open-access platform for detailing, sharing, and discussing molecular and computational protocols that can be useful before, during, and after publication of research results.

VERVENet capabilities to go viral

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 to release novel protocols for studying marine microbes. The 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.

My Bioinformatics Cookbook

Screen Shot 2015-11-12 at 3.31.25 PM 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 (akin to Github). This work has been done through the VERVENet project (Hurwitz Lab) in collaboration with the team at

OpenCloud for open science

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.

Groups in


Now that we have ironed out most of the bugs through the VERVE Net, we are opening up the group functionality in 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 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 *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.