Bringing software to the phage field

Issue 58 | January 3, 2020
8 min read
Capsid and Tail

The code for Capsid & Tail, taken at Switchyards, Atlanta. Photo credit: Jan Zheng / Phage Directory

Happy New Year, phage enthusiasts! This week, we share how we plan to help the phage research community systematize and standardize phage data collection in 2020.

What’s New

BBC News has listed Isabelle Carnell Holdaway’s phage therapy case as one of the biggest ‘Man on the Moon’ breakthroughs of 2019.

NewsPhage Therapy

Cytophage Technologies is an up and coming phage biotech company out of Winnipeg, Canada: here’s an introduction (including how the founder treated his own foot with phages, and plans to start by breaking into the poultry market). News story: Financial Post

NewsBiotech

A Minnesota man’s leg amputation was prevented by phages from Adaptive Phage Therapeutics. News story: Star Tribune

NewsPhage Therapy

New paper in Evolution by Animesh Gupta (UCSD) and colleagues: lambda phage overcomes a perturbation in its host-viral genetic network through mutualism and evolution of life history traits.

Research

New bioinformatics tool published by Qiaoliang Liu (Jilin University) for identifying phages from metagenomic bins and contigs: Virus Finding & Mining (VFM).

Bioinformatics Tool

Latest Jobs

Ridge Vineyards Inc in Cupertino, CA is seeking a viticultural intern for a phage project.
Texas A&M is seeking a technician to work on phage projects.
The J. Craig Venter Institute in Rockville, MD seeks a postdoc to develop improved reverse genetic tools for viruses (phage work involved).
Johnson & Johnson seeks a Microbiology Leader, Scientific Director (phage work involved).
The Mikaelyan lab at North Carolina State University seeks a new postdoc to pursue original projects involving termite-microbe interactions (phage work involved).

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

The community board is empty this week. Be the first to post something for next week!

Bringing software to the phage field

Profile Image
Phage microbiologist and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

We spent the last year visiting phage labs and companies, and talking to phage researchers about what they need to make their phage work easier. Something that kept coming up was a need for database and software support.

Research teams around the world are collecting and characterizing large libraries of phages, they’re sharing them with each other, and they’re using them in patients. Companies are looking for well-characterized phages they can screen as they develop products. But what’s the best way to keep track of all this data? Can we all be collecting the same kind of data, in the same way, so we can compare our phages and draw new information from the patterns we see?

We want to tackle this problem and create the software infrastructure the phage field is currently missing. We can’t do it alone, but based on the enthusiasm we’ve felt from the phage community, we’re excited to build solutions that help the community handle the rapidly expanding body of knowledge we’re accumulating about phages.

Tracking phages and standardizing phage data collection

In mid-2019, we received a Mozilla Open Science grant to start designing a global phage catalogue and a platform for publishing phage data. It was thanks to these funds that we were able to spend most of the year traveling to meet with phage labs so we could get their input early on.

We heard about many challenges, especially for labs involved in phage therapy cases. Some labs are finding themselves with increasing numbers of phages and strains in their collections, many of which came from academic, commercial or clinical collaborators, sometimes with separate terms of use documents for nearly every sample. Other labs have plans to develop well-characterized phage libraries, but keeping track of each phage’s characteristics is already becoming difficult to manage.

Overall, we heard that researchers want better ways to keep track of their phages, and better ways to find out what’s being learned about other phages. People want agreed-upon standards for phage characterization, and they’re willing to help set them. And they want to be able to safely share phages without being overwhelmed by paperwork and uncertainty. We think we can help make these desires a reality, with the help of the global phage community.

Which phage characteristics matter to you?

We want to build a phage database system that accomodates both the data phage labs are already collecting and the data they aspire to collect. Are you already building a phage database? Or thinking you might need one someday soon? We’d love to hear from you about what matters to you when it comes to phage data collection.

Ready to track your phages?

We are ready to collaborate directly with phage research groups to create software customized to your projects. Essentially, Phage Directory can be your software partner; we can build and implement systems according to what you need, and help you figure out what that is.

If systematizing your phage data collection is something you’re interested in, either now or as part of a future project, please reach out to us!

Continuing to cultivate the phage community

As we shift toward building software-based tools, we are more committed than ever to continuing to build up a global community of professionals working with and interested in phages.

To do this, we’ll be continuing to publish and improve Capsid & Tail, fostering collaboration through our community message board and directory, maintaining our phage sourcing tool, and continuing to support phage conferences through live updates and post-event recaps. Beyond this, we’re always open to new ways of fostering community in this field.

In summary: our goal for 2020

Phages have so much potential, but we can’t use them without understanding what they’re good for, when to use which, and how to employ them. We want to make it easier to pick the right phages for any situation. The phage community knows that to do so, we need to have the data. While there’s still a lot we don’t know about phages, we should be thinking not only about doing more research, but also about how we’re collecting the data and making it accessible. As in any industry, too much unorganized data can cause problems. Not only would it be a shame to underutilize all the data we have, but we’d be missing an opportunity to draw patterns from the data if we didn’t regularly analyze it in aggregate. In 2020, we want to help the phage community establish standards and systems to collect data on phages, bank these phages, and make the phages and the data quickly accessible.

Here’s to a fantastic year ahead!
— Jessica and Jan

Some 2019 accomplishments we’re proud of:

  • Nearly quadrupling our number of Capsid & Tail subscribers (from 202 this time last year to 726)! To put that number in perspective, the number of researchers who attend phage conferences generally ranges from 200-500
  • Drastically improving the breadth of Capsid & Tail’s reach: we now reach phage researchers in 72 countries!
  • Creating a Capsid & Tail guest writer program, and publishing 20 fantastic guest-written articles!
  • Opening up Phage Directory to all phage professionals, organizations and labs (not just those involved in phage therapy), and more than doubling our number of listed phage professionals (from 55 to 133)
  • Authoring two peer-reviewed perspectives on compassionate phage therapy (in Viruses and Microbiology Australia), and one invited book chapter
  • Obtaining a Mozilla Open Science grant to support our mission to make phage research and development easier
Capsid & Tail

Follow Capsid & Tail, the periodical that reports the latest news from the phage therapy and research community.

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Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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