phylotastic hackathon (Jan 28 - Feb 1, Tucson, AZ) of possible interest to galaxy developers
Dear galaxy developers--
I'd like to bring your attention to the call for participation included below this message. A "Phylotastic" system is a distributed tree-of-life delivery system composed of web services. Although it is not readily apparent from the presentation linked below, the project includes some work on using Galaxy as a framework for managing a phylotastic workflow. See the demos page (http://phylotastic.org/demos.html) and the "Making Galaxy Phylotastic!" screencast (http://youtu.be/kMME658xOu4 for more.
I would be happy to respond to questions about the project. Please consider applying if you are excited by the project and think that you can contribute. Regards,
Arlin ----- Phylogenies! Hacking! Tucson in January!
An implicit promise of the Tree of Life project is that, ultimately, expert knowledge of species phylogeny will be accessible and usable by everybody. In other words, we will all be able to get the species trees we need, in a useable form, when we need them. The Phylotastic project aims to make that vision a reality, by developing a loosely coupled system of components that, in response to a user’s query (a list of taxa plus conditions), will rectify names, find suitable source trees, prune and graft to get the right species, estimate branch lengths, and return the results with metadata on sources and methods.
In June 2012, the HIP (Hackathons, Interoperability, Phylogenies) working group of NESCent staged a hackathon (http://en.wikipedia.org/wiki/Hackathon) to prototype components of a Phylotastic system, and implement demos to show their potential. Thanks to 25 participants who responded to an open call (just like this one), that hackathon was an extraordinary success (see http://phylotastic.org/).
Now we are gearing up for a second hackathon, to take another step toward providing computable, convenient, credible access to the Tree of Life. We aim to recruit a diverse group of participants, including students, faculty, postdocs, and staff of both genders and from different backgrounds. Only some of the seats at the hackathon will be filled by expert hackers who spend their time coding. We also need folks who can:
* Provide knowledge of workflows and downstream uses of trees * Design user interfaces * Test software * Make screencasts, develop tutorials, and document user experiences
Applications are now being accepted to Phylotastic 2, which will take place January 28th, 2013 to February 1st, 2013 at the BIO5 facility in warm and sunny Tucson, AZ (http://bio5.arizona.edu/about-bio5). Information on how to apply is provided below. Partial support (and, if funds allow, full support) for travel, food and lodging will be available to each successful applicant who indicates need. We particularly welcome applications from women and members of underrepresented groups.
To understand how you might be able to contribute, review the slideshow (ppt format, http://bit.ly/RWRgIc, or PDF format, http://bit.ly/POaoci), consult the web site (phylotastic.org) or contact a member of the HIP leadership team (listed below).
Sincerely,
the HIP (Hackathons, Interoperability and Phylogenies) Leadership Team
HOW TO APPLY Before 16 November, 2012 at midnight, EST, fill out the online form here http://tinyurl.com/PhyloTastic2. Note that:
* The application form asks you to describe how you can contribute to Phylotastic. Remember that we are not just looking for expert coders. There are many other ways to contribute. * Support for travel, housing and meals will be available to each successful applicant who indicates need. * Please understand that your application is not a guarantee of participation in the event. Funds and space are limited: we may not be able to sponsor every individual who is qualified to participate.
LEADERSHIP TEAM Karen Cranston, karen.cranston@nescent.org Brian Sidlauskas, brian.sidlauskas@oregonstate.edu Arlin Stoltzfus, arlin@umd.edu Mike Rosenberg mrosenb@asu.edu Brian O’Meara, bomeara@utk.edu Mark Westneat mwestneat@fieldmuseum.org Enrico Pontelli epontell@cs.nmsu.edu Rutger Vos rutgeraldo@gmail.com Naim Matasci nmatasci@iplantcollaborative.org
------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850 tel: 240 314 6208; web: www.molevol.org
Arlin, this sounds great. There have been a few discussions on the list over the last two weeks about Phylogenetic tools, it would be great if the groups responsible could send representatives to the hackathon to coordinate. My group would definitely like to send at least one Galaxy core team member to participate. But if we can get some more people from the Galaxy+Phylogenetics community we can get a lot more done I'm sure! -- jt
On Tue, Oct 30, 2012 at 1:36 PM, Arlin Stoltzfus arlin@umd.edu wrote:
Dear galaxy developers--
I'd like to bring your attention to the call for participation included below this message. A "Phylotastic" system is a distributed tree-of-life delivery system composed of web services. Although it is not readily apparent from the presentation linked below, the project includes some work on using Galaxy as a framework for managing a phylotastic workflow. See the demos page (http://phylotastic.org/demos.html) and the "Making Galaxy Phylotastic!" screencast (http://youtu.be/kMME658xOu4 for more.
I would be happy to respond to questions about the project. Please consider applying if you are excited by the project and think that you can contribute. Regards,
Arlin
Phylogenies! Hacking! Tucson in January!
An implicit promise of the Tree of Life project is that, ultimately, expert knowledge of species phylogeny will be accessible and usable by everybody. In other words, we will all be able to get the species trees we need, in a useable form, when we need them. The Phylotastic project aims to make that vision a reality, by developing a loosely coupled system of components that, in response to a user’s query (a list of taxa plus conditions), will rectify names, find suitable source trees, prune and graft to get the right species, estimate branch lengths, and return the results with metadata on sources and methods.
In June 2012, the HIP (Hackathons, Interoperability, Phylogenies) working group of NESCent staged a hackathon (http://en.wikipedia.org/wiki/Hackathon) to prototype components of a Phylotastic system, and implement demos to show their potential. Thanks to 25 participants who responded to an open call (just like this one), that hackathon was an extraordinary success (see http://phylotastic.org/).
Now we are gearing up for a second hackathon, to take another step toward providing computable, convenient, credible access to the Tree of Life. We aim to recruit a diverse group of participants, including students, faculty, postdocs, and staff of both genders and from different backgrounds. Only some of the seats at the hackathon will be filled by expert hackers who spend their time coding. We also need folks who can:
- Provide knowledge of workflows and downstream uses of trees
- Design user interfaces
- Test software
- Make screencasts, develop tutorials, and document user experiences
Applications are now being accepted to Phylotastic 2, which will take place January 28th, 2013 to February 1st, 2013 at the BIO5 facility in warm and sunny Tucson, AZ (http://bio5.arizona.edu/about-bio5). Information on how to apply is provided below. Partial support (and, if funds allow, full support) for travel, food and lodging will be available to each successful applicant who indicates need. We particularly welcome applications from women and members of underrepresented groups.
To understand how you might be able to contribute, review the slideshow (ppt format, http://bit.ly/RWRgIc, or PDF format, http://bit.ly/POaoci), consult the web site (phylotastic.org) or contact a member of the HIP leadership team (listed below).
Sincerely,
the HIP (Hackathons, Interoperability and Phylogenies) Leadership Team
HOW TO APPLY Before 16 November, 2012 at midnight, EST, fill out the online form here http://tinyurl.com/PhyloTastic2. Note that:
- The application form asks you to describe how you can contribute to
Phylotastic. Remember that we are not just looking for expert coders. There are many other ways to contribute.
- Support for travel, housing and meals will be available to each successful
applicant who indicates need.
- Please understand that your application is not a guarantee of
participation in the event. Funds and space are limited: we may not be able to sponsor every individual who is qualified to participate.
LEADERSHIP TEAM Karen Cranston, karen.cranston@nescent.org Brian Sidlauskas, brian.sidlauskas@oregonstate.edu Arlin Stoltzfus, arlin@umd.edu Mike Rosenberg mrosenb@asu.edu Brian O’Meara, bomeara@utk.edu Mark Westneat mwestneat@fieldmuseum.org Enrico Pontelli epontell@cs.nmsu.edu Rutger Vos rutgeraldo@gmail.com Naim Matasci nmatasci@iplantcollaborative.org
Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850 tel: 240 314 6208; web: www.molevol.org
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Arlin Stoltzfus -
James Taylor