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Introducing Supercell

Introducing Supercell

You may have already seen the news from our friends at Facebook, but just in case it passed you by, the OSU Open Source Lab (OSL) is excited to announce our newest project: Supercell. Supercell is a new on demand virtualization and continuous integration resource, made possible by a generous grant from Facebook's Open Source Team. We have created this cluster for use by open source projects who need to run software tests regularly but may not have access to the appropriate hardware or the funds to pay for outsourcing this service. Supercell will also allow projects to do manual testing to verify that a submitted patch has actually fixed the intended bug or to determine that their software package runs correctly on a particular operating system or distribution. The service will also allow projects to test their software in a large cluster using several VMs concurrently. Supercell will also provide temporary space for projects who would like to test drive new features in their code base or on their website.

Supercell: Finding your bugs before they spiral out of control

Cluster management in Supercell is done using Google's Ganeti on top of Linux KVM. We will also provide users with access to manage their own clusters using Ganeti Web Manager, a homegrown project of the OSL built using Django. We're incredibly proud that Supercell has been built using a 100% open source software stack.

You can find out more about Supercell by visiting the project FAQ. Supercell is currently in early alpha for testing purposes, but will be available for use by open source projects in Q3 2011. You can stay tuned to progress on the Supercell project by giving us feedback on how you'd like to use it and requesting to subscribe to our announcement list.

If you're looking for more detail about Supercell "under the hood", you can follow @ganetiwebmgr on Twitter. For more in-depth information, our Lead Systems Administrator/Architect, Lance Albertson has written an article about all the features in the latest release of Ganeti Web Manager, and our Lead Developer, Peter Krenesky, has blogged about the permissions system. You can also learn more about how the OSL uses Ganeti to manage our clusters on Lance's blog.

Google Code-in: Our Results are In!

Google Code-in: Our Results are In!

The Oregon State University Open Source Lab (OSL) participated for the first time in the Google Code-in (GCI) contest, and we're pleased to report that the results of the contest were incredibly valuable for us. If you haven't heard about Google Code-in, it's a contest run by Google's Open Source Team that aims to introduce pre-university students to all aspects of open source software development. (For more details, check out the excellent summary on the Oregonian's Higher Education Blog.) We had eight students actively working with us in GCI, from as far afield as Australia and Poland. Of these eight students, two have let us know they plan to keep working on projects with the OSL and one even let us know that he's hoping to attend Oregon State University so he can learn even more about open source and help out at the lab.

We had a total of 42 tasks completed, all improvements to Ganeti Web Manager, a homegrown project of the OSL. For those who aren't familiar with the project, it's a Django based web application that help administrators better manage their Ganeti-based clusters. Our students completed a total of 42 tasks: 23 coding tasks, 18 tasks to improve Ganeti Web Manager's user interface, and one outreach task (logo design). We were especially excited that our students found several unknown bugs in our code base and proceeded to send us fixes for them. You can take a look at all of the tasks proposed by the Lab and all those completed by our students on the contest website.

As a result of participating in Google Code-in, several major features were implemented in Ganeti Web Manager, including:

Of all these major features, creating the status dashboard was the most difficult of our tasks. We required a very concise layout for the feature and the student working on the task was not a native English speaker, but he did an outstanding job. In fact, if you'd like to get to knw the student who worked on the dashboard, we've already published an interview with Piotr for your reading pleasure.

We also noted down some observations about the contest that we'd like to share in case they are useful to the community in planning for any future GCIs. We had about 10 students sign up for difficult tasks and simply never submit any work for them, though in two cases the students submitted an initial set of work and then did not follow up after receiving feedback. We're wondering if other folks had this experience and what they did to mitigate it. We certainly did our best to be available as much as possible either via email or on IRC. We're very happy with what our students accomplished, though, so perhaps its just that those students who abandoned the tasks found they weren't the right fit for them and didn't know to withdraw their claim.

We've found that GCI was far more work for our mentors than our participation in Google Summer of Code, though in some ways it also much more productive. Our mentors found it easier to select smaller, bit-sized projects for students to work on, though that also meant a lot more work to review their output in a short period of time. One of our mentors notes that the value of GCI is in that same rapid pace, though; if a student discovers that a task is not to his liking or the mentor realizes she may have sent the student off in the wrong direction, it's a quick fix to send the student along to the next task or to a different mentoring organization that may better match the student's interest. With a 3-month long coding project, it's less easy to be agile in deciding when to rework the project or when it is best to simply not complete it.

Overall, we were incredibly excited to be a part of GCI and extremely pleased with our results. We certainly hope to continue mentoring for the contest, assuming Google chooses to run it once again. Many thanks to all of our students for their great work and many thanks to Google for doing awesome work to promote student involvement in open source!

OSL Newsletter: A Look Back at 2010

OSL Newsletter: A Look Back at 2010

We’ve had plenty of good things happening at the OSL since we brought your our last newsletter, and as we’re busy gearing up for 2011 we wanted to take a few moments to share our good news with the community.

First, the best news: We’re Hiring!

The OSL is hiring for a full-time software developer who will analyze, design, and test software code for Ganeti Web Manager, the Protein Geometry Database and several other homegrown Open Source Lab projects. For more details on the position and instructions on how to apply, check out the Analyst Programmer role on the Oregon State University Jobs page.

Wrapping our Sixth GOSCON

Producing the Government Open Source Conference has been a six year labor of love for the OSL team and, in particular, Deborah Bryant, our Public Sector Communities Manager. We were excited that GOSCON returned to Oregon for its sixth instance, and even more excited when the City of Portland declared the week of the conference "Open Source in Government Week." Attendees were treated to more than twenty talks on all aspects of the use of open source in government, from agency use cases to panels on how to meet the challenges of open government initiatives. You can find a full post-conference write up on the GOSCON website and stay tuned to all things GOSCON by following @goscon on Twitter.

We've posted many of the slide sets from the conference presentations, and will be adding more as we continue to receive them from speakers. Stay tuned for an announcement that videos from the sessions are available, though you can already enjoy some video interviews with speakers and attendees from OpenAffairs. You can also check out talks from the world's first IgniteGov on YouTube, and you might be interested in Alex Howard's O'Reilly Radar write up on the talk "Why middleware is the key to a successful gov 2.0" from Portland's very own CivicApps contest winner and Code for America Fellow, Max Ogden.

Developer News

Our developer team has been hard at work adding new features to Ganeti Web Manager, putting out the 0.4 release on December 22nd. New features include improvements to the caching system, SSH key feeds, import tools and more. You can learn more about Ganeti Web Manager's permissions system on the blog of our Lead Developer, Peter Krenesky. For details on how the OSL uses Google's Ganeti to manage our clusters, check out the writings from our Lead Systems Administrator/Architect, Lance Albertson.

We've also created a Twitter stream for Ganeti Web Manager news, @ganetiwebmgr. Follow us for more news and announcements about upcoming GWM talks.

In addition to working on Ganeti Web Manager, Peter and our team of student developers have been hard at work on a new tool for researchers, the Protein Geometry Database. The PGD gives researchers robust and straightforward ability to analyze 16,000 non-redundant protein chains, their backbone conformation and geometry, as well as the relationships between them. You can learn more about the academic uses and the development process for the PGD in one of our recent news articles, or check out the technical documentation and source code at

Google's Open Source Programs for Students

The OSL has been a proud participant in Google's open source programs for students since 2006, our first year participating in Google Summer of Code. This year we had two students successfully complete their projects, both of them working on Pydra, a distributed and parallel computing framework for Python. Once again, one our student employees mentored for the OSL this year, with Corbin Simpson working with Bartosz Wroblewski on Implementing Map Reduce in Pydra. Brian Martin worked with Peter on a whole wishlist of features for Pydra's 1.0 release. Congratulations to Bartosz and Brian, and many thanks to them for working with us for Google Summer of Code 2010.

In addition to our participation in GSoC, we were one of twenty mentoring organizations selected to participate in Google's second contest to get pre-university students involved in open source, Google Code-in. We're less than seven days away from the contest closing, and we've been incredibly pleased with our results: more than 30 tasks have been completed to improve Ganeti Web Manager, ranging from bug fixes, creating new features to improvements to the user interface. We've published an interview with one of our most prolific GCI students, Piotr, for your further reading pleasure. You might also want to read the post from our Project Manager, Greg Lund-Chaix, on the valuable experience provided to students participating in the contest.

Many thanks to Google and their Open Source Team for sponsoring these great programs!

Welcome to Our New Hosted Communities

Over the past six months, we've welcomed more than ten new projects to the OSL, including:

  • Elgg, an open source social networking engine
  • FOSSFA, the Free Software and Open Source Foundation for Africa, a group charged with promoting the use of the FOSS model in African development and integration and adoption of FOSS in Africa's national policies
  • Funtoo Linux, a Gentoo Linux variant personally developed by Daniel Robbins, creator of Gentoo Linux
  • The Genomics Standards Consortium, an open-membership, international working body to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data
  • Mageia, a fork of Mandriva Linux, supported by a not-for-profit organisation of recognized and elected contributors
  • OAGITM, the Oregon Association of Government IT Management, a statewide association of information technology managers for City, County, State, and other affiliated government agencies within Oregon
  • OSGeo, the Open Source Geospatial Foundation, a not-for-profit organization whose mission is to support and promote the collaborative development of open geospatial technologies and data
  • PDX11, a collaboration hub for the City of Portland, Oregon's economic development initiatives related to the software industry
  • Teaching Open Source, a vendor neutral collaboration site for professors, institutions, communities, and companies to come together and make the teaching of open source a global success

The OSL and Humanitarian Free and Open Source Software

We also welcomed two new humanitarian focused communities to the OSL family, CrisisCommons and the Sahana Foundation. CrisisCommons is a group of individuals collaborating on a commons-based approach to disaster relief and crisis management, most notably through their CrisisCamp events. CrisisCommons announced the move of their infrastructure to the OSL as part of their receipt of a $1.2M grant from the Sloan Foundation.

The Sahana project was initiated by volunteers in the Sri Lankan FOSS development community to help their fellow countrymen and countrywomen affected during the 2004 Asian Tsunami in December 2004. Since its inception, Sahana has been rewritten as a set of modular disaster management tools, including a Missing Person Registry, an Inventory Management application and a Volunteer Coordination system.

You can read more about Sahana and two other OSL hosted Humanitarian FOSS communities, OpenMRS and TriSano, in the December issue of the Open Source Business Resource magazine on Humanitarian Open Source. Leslie Hawthorn, our Open Source Outreach Manager, guest edited the issue.

Sharing Stories

We're excited to share all this great news with the community, but we want to hear from you. What stories from the OSL would you like to hear? What's going on in our hosted communities that we ought to be communicating to the wider OSL community? Send your thoughts to us on Twitter, Facebook or by email to Leslie Hawthorn at leslie at osuosl dot org

About this Newsletter

This newsletter contains updates of recent events at the Oregon State University Open Source Lab. We will continue to publish newsletters every 3-6 months in the future. Newsletters will be posted to our website as well as sent out to an email list. If you'd like to receive newsletters via email, please sign up at

We're Hiring: Full-Time Developer Opening in Corvallis, Oregon

We're Hiring: Full-Time Developer Opening in Corvallis, Oregon

Want to write code and support the missions of some of the world’s most important open source projects?

Oregon State University’s Open Source Lab is recruiting a full-time software developer who will analyze, design, and test software code for Ganeti Web Manager, the Protein Geometry Database and several other homegrown Open Source Lab projects. Development at the OSL includes collaborations with academic and research faculty internal and external to OSU.

Reporting to the Operations Manager of the Open Source Lab, the Analyst Programmer will contribute in-depth knowledge of open source software development using languages such as Python, Ruby and Java. The person in this position is responsible for developing and modifying complex software applications, documenting code and development processes, and overseeing student software developers. This position will allow the candidate to interact with many of the open source projects hosted by the OSL. We seek candidates with a high level of initiative, motivation, and a high degree of success in previous endeavors.

To review more a more detailed job description and apply, check out the Analyst Programmer role on Oregon State University's Jobs page.

The Protein Geometry Database: a new tool for researchers

The Protein Geometry Database: a new tool for researchers

The OSU Open Source Lab (OSL) and the OSU Department of Biochemistry and Biophysics have recently collaborated to create a database of protein geometry as a tool for researchers. Named the Protein Geometry Database (PGD), the database gives researchers robust and straightforward ability to analyze 16,000 non-redundant protein chains, their backbone conformation and geometry, as well as the relationships between them. OSU Professor and Chair of the Department of Biochemistry and Biophysics, Dr. Andrew Karplus, graduate student, Dr. Donnie Berkholz, and Postdoctoral Fellow, Dr. Dale Tronrud, provided the scientific knowledge for this first-of-its-kind program. OSL head software developer Peter Krenesky and OSL student developers John Davidson, Ani Ovsepyan, Sean Connell and Scott White supplied the technical skill.

“Proteins are important. Pretty much everything that happens in life, there's a protein for that,” says Karplus. “Proteins carry out their function because of their structure, so knowing how they look makes it easier to see what they do."

Dr. Karplus and his team had a rough version of the PGD before they approached the OSL for help, but searches through it could take hours. The database also had a fairly primitive user interface that was extremely difficult to use. The OSL team rewrote the PGD in Python using Biopython libraries, a set of freely available tools for biological computation. To deal with the congestion and overloading that occurred when statistical calculations were performed on the database, the developers used Django's aggregation functions to keep the data in one place while working with it.

The PGD is the first protein geometry database that analyzes protein geometry and conformation together. This results in more accurate angles, which allows researchers to create more accurate models of the protein's structure. “Deciphering how protein structure works and its linkage with function has important implications for our ability to understand how our body works at the smallest scale and to determine the molecular basis of diseases,” said Berkholz, who relied on the PGD's ability to complete complex, fast database searches to complete his thesis research.

Karplus and his team used the PGD to prove that protein bond angles depend on conformation. This brings to the field of protein structure a completely new level of understanding. You can learn more about their findings and the PGD in the following papers