 | Eamonn Maguire on Toward interoperable bioscienc… |
 | Geordie Pele on ISA tools code dashboard |
| Eamonn Maguire on Compared to what? The ArrayExp… |
 | Misha Kapushesky on Compared to what? The ArrayExp… |
 | qwerty on The MAGE to ISA converter take… |
All of our tools are being ported over to Travis CI, so now you’ll be able to see the builds of the tools for ISAcreator, BII, etc. on every commit, and also see the current build status directly from each GitHub page.
ISAcreator build status now more visible. This is happening now for all our tools incrementally over the next few weeks.
We are close to releasing new versions of all the tools, with many features added and many things improved, including performance! Message coming soon via our isaforum mailing list (see http://isatab.sourceforge.net/contact.html for details on joining this list).
^ *([\w_]+(?: *[\w/_\-\: ]+)? *) *(?:\[ *([\w_]+(?: *[\w/_\-\: ]+)? *)* *(?:\( *([\w_]+(?: *[\w/_\-\: ]+)? *|\b(((\S+)?)(@|mailto\:|(news|(ht|f)tp(s?))\://)\S+)\b) *\))?\])? *$Not my largest regex by any means, but it looks complicated
Are you a student interested in evolutionary biology and open-source software development?
PHYLOINFORMATICS SUMMER OF CODE 2012
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012
The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program receive a stipend from Google (and the coveted T-shirt upon completion!), and work from their home, or home institution, for the duration of the 3 month program. You will have to opportunity to collaborate with our enthusiastic mentor community, and will have at least one dedicated mentor to help you complete your project. We are particularly targeting students interested in both evolutionary biology and software development.
Our website, above, lists potential projects. Projects include many programming languages (e.g. C/C++, Java, Perl, R) and cover subjects ranging from visualization to algorithm implementation to data interoperability. You don’t need to be an expert in either evolutionary biology or software development – find a project idea that interests you, and we can work with you to develop a proposal that fits your skills. We also welcome novel project ideas apart from those already on the list.
INTERESTED? Contact us phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Admission is competitive, and we want plenty of time to work with you to develop a great project proposal.
TO APPLY: Apply online at the Google Summer of Code website: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 where you will also find GSoC program rules and eligibility requirements. The 14-day application period for students opens on Monday March 26th and runs through Friday, April 6th, 2012. Google Summer of Code FAQ: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs
I stumbled across Saliency from the Perceptual Science Group @ MIT.
It identifies, given some web page, the important regions of your page, from what I can tell, it focuses on bright regions. The results are presented in a blacked out page, highlighting the ‘salient’ regions.
Information about how the algorithm works is available from here.
There’s nothing kinky here, so you’ll be incredibly disappointed if you choice of search words has led you to this blog post.
I’ve been doing some relatively complicated tables in Latex recently and then stepped upon this lovely piece of software called Calc2Latex…it is a macro/plugin/whatever you want to call it for OpenOffice which can take your table, with row/column merges and all, and produce the Latex version…so no struggling with multicolumns etc. It saved me an amazing amount of time today!
Our commentary, named “Toward interoperable bioscience data” has just been released in Nature Genetics. In it, we focus on working towards an ISA commons, where one day we’ll all be able to share our experimental metadata in one common, easy to use format, supporting minimal information checklists and ontologies (via the ISA-Tab format and respective tools).
The editor speaks about the paper, paraphrased here:
“Reformatting data is a full-time job for many researchers, even before the minimum reporting guidelines, terminologies and formats of each field are taken into consideration. In this issue, we present a Commentary and a Perspective suggesting solutions to these problems that have been developed by a process of community consultation and open review to which the journal was a party. In the Commentary, Susanna-Assunta Sansone and colleagues identify one central problem, namely that “most repositories are designed for specific assay types, necessitating the fragmentation of complex datasets,” and they offer a unified view of the metadata formatting that will be needed to ensure that biomedical research datasets become interoperable. This solution is the overarching ISA framework, where the acronym stands for ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) (p 121). This proposal shifts the sets of reporting standards agreed upon by each community into the infrastructure and formatting of the data files themselves. Sansone and colleagues also list a set of participant communities that can pioneer the approach and teach by example.”
Many thanks to all who contributed to the paper and to the growing success of ISA (commons and tools).
We are hiring! Details are below:
University of Oxford, UK
Software Engineer (3 year fixed term) start date April 2012, or asap
Complete applications must be received by 12 noon on 15th February 2012
Interviews will held between 22nd and 28th February.
Salary: £29,099 – £35,788pa (grade 7)
Location: Oxford e-Research Centre, 7 Keble Road, Oxford, UK
Projects: http://www.isa-tools.org and http://www.biosharing.org
Other entitlements: 38 days’ annual leave including public holidays and Christmas closure
Membership of the University’s Pension Scheme
We are seeking an enthusiastic, experienced Software Developer to engage in software development and to contribute to successful projects on standards and data sharing infrastructure for management, curation and sharing of bio-investigations.
The following criteria are considered essential to the post:
• degree in a relevant field, such as computer science or bioinformatics, ideally with some background knowledge in biology
• proven professional experience and profound knowledge of Java
• ability to work efficiently as part of a distributed development team
• experience in the design and/or implementation of distributed software
• willingness to work as part of a team and demonstrated flexibility to respond to emerging needs
The following criteria are considered to be desirable though not essential
• Oracle, MySQL, JBoss, JBoss Seam, Lucene, AJAX, JAXB, XML schema, RDF, SPARQL, Java Script, PHP, Python
• experience of development for and testing on Windows, Mac OS X and Linux operating systems
• understanding of software development lifecycle and agile development methodologies
• ability to perform user requirements analysis
More details and link to application form at: https://www.recruit.ox.ac.uk and enter Vacancy ID: 101935
We’ve just added a code dashboard to the website so that you easily see the commit activity across all projects (most active projects are at the top and change dynamically). The page is powered by Gitview (http://gitview.logicalcognition.com/).
ISAcreator dashboard page
We hope to add extra information to each box about current build status (retrieved from our TeamCity continuous build management system), latest releases and issues currently being reviewed discussed at any point in time.
Please let me know if you experience any rendering problems in your browser.
Deein canny son
The Harvard Stem Cell Discovery Engine (SCDE) is now published in NAR. The SCDE is one of many systems now utilising the ISA tools and ISA-Tab format. Check out the publication.
Geordie Pele is discussing. 
This is now Open Access!!