due to the new WormBase web interface (preview it on Beta WormBase) scaling dynamically with demand and location of requests, dedicated permanent mirror sites will become obsolete as soon as the new infrastructure is deployed.
As part of this, wormbase.sanger.ac.uk will be retired on the 25th November 2011.
We’re hiring. You want to do web architecture development in support of a project essential to basic biomedical research.
The Ontario Institute for Cancer Research seeks an agile and adaptable software engineer with a broad skill set and an interest in applying it to scientific problems. You will assist the team in designing and implementing a scalable architecture and web interface to a vast array of biological data supporting a global community of researchers. This position will be based in Toronto, ON, Canada.
We’re looking for someone excited about science, computers, and technology. You’re comfortable working with big data and moving information between formats, systems, and platforms. You are passionate about trending technology and social media and how they might enhance the scientific process. You can work within the constraints of legacy systems when required and in proposing and evaluating new alternatives when warranted. In the past, you’ve confronted issues related to scalability and data management and have created demonstrable solutions resolving them.
As a web developer, you possess a broad range of skills that you’ve used to generate maintainable and stable solutions. You’ve deployed or considered things like EC2, Hadoop/Hoop/HBase/HDFS, Map/Reduce, and NoSQL variants for data management and analysis. You speak Perl fluently, know what Moose look like, have heard of Catalyst, use MySQL and interact with it via ORMs, and love git. You actually enjoy writing documentation and tests. You’re not a designer, but can write HTML and CSS when necessary, know some Javascript and the basics of Ajax. When required, you can jump in and help out on a variety of tasks that might not immediately fall under your purview as the needs of the project evolve. Strong candidates will have an understanding of modern biological concepts and familiarity with open source bioinformatics tools like BioPerl and GBrowse. Those from other non-biological science backgrounds but with strong software engineering skills will also be considered.
We’re a small, dedicated, distributed team. You should work well independently, and be receptive to exchanging ideas via IM, Google Hangouts, Skype, social media outlets, conference calls, and email threads. In short, excellent communication skills are assumed.
Experience:
Bachelors degree in Computer Science, Bioinformatics, Biology or related field with a minimum of three years experience. On the upper end, a Masters or PhD with 3-5 years suitable experience.
Please send resumes and vitaes to [email protected].
We’re simultaneously upgrading the storage architecture and request routing of WormBase starting today (Friday) running through Saturday afternoon. We’ve made preparations to keep all services available during this maintenance period. Intermittent service interruptions are possible, however, as these changes propagate across the global DNS network. We apologize for any inconvenience.
Today, we’re excited to announce the opening of the public beta test period for the next generation WormBase website!
The new website has been redesigned from the ground up with the following objectives:
* Easily handle many species and populations;
* Present the full extent of experimental data in C. elegans in customizable displays without presenting overwhelming amounts of unrequested data;
* Engage users with new opportunities for directly adding, commenting on, and correcting annotations;
* Provide support for under-served research communities;
* Be accessible to users from different backgrounds (researchers, educators, students);
* Be rock solid, stable, maintainable, and easy for anyone to extend;
* Be fast and easy to scale as demand warrants and database size increases.
Here’s a short list of some of the site’s features:
* Customizable content: pick what you want to see, ignore the rest;
* Customizable layout: arrange and rearrange as you see fit;
* Create an account and save your favorite items, or use a Google, Facebook, or Twitter account;
* Entirely new, more informative displays that make it faster to get desired information in fewer clicks. See, for example, the allele listing on the Gene Summary;
* History tracking;
* Persistent site preferences from device to device;
* Public comments and issue reporting;
* Direct chat with curators;
* Powerful new global database search option;
* For data miners, a complete RESTful API: every piece of information in WormBase uniquely addressable. More on this in subsequent blog posts.
Although we’re really excited to introduce the site, please do watch your step.
There are many features that we are actively working on and many more that we will be rolling out shortly. We are also gauging real-world performance so that we can make improvements and enhancements to the architecture before the public production release in January. That said, we think that at its current state of development, the site is stable, useable, and useful.
You can report issues and leave comments (eg on the glr-1 page) for WormBase staff and other researchers directly on the site.
And if you have a chance, please take our User Survey.
We have a huge number of new features and enhancements in store for the new website, but we wanted to get the site in your hands now to start collecting feedback on the content and look-and-feel.
Be sure to leave comments and report issues! And if you or your lab are interested in participating in focus group testing, please drop me a line ([email protected]).
September – November: Iterative development and testing; focus groups
January 2011 – Launch new website on www.wormbase.org
April 2012 – Retire original WormBase site