Tuesday 25 September 2012

Field and Laboratory Information Management Guide Published for DNA Barcoding Methods


Two chapters in Volume 858 of Methods in Molecular Biology have been published that assist users in managing Field and Laboratory data for DNA Barcoding:

Field Information Management Systems for DNA Barcoding (Deck, et al)
Instructs users how to use the Field Information Management System (FIMS) developed for the Moorea Biocode Project to use for their own project, including steps on integrating with a Laboratory Information Management System.

The Laboratory Information Management System chapter gives instruction on how to use the software for managing contextual data for samples, connecting to FIMS, and tracking workflows throughout the lab life cycle.


Saturday 23 June 2012

Biocode Commons at the GSC14 Hackathon

There will be two hackathon tracks at the GSC14 Conference in Oxford from Sep 19th through 21st. 

The first hackathon will happen from Wednesday afternoon and all day Thursday and will create an ontology to track collecting events, samples, organisms, sequences, and identifications related to Ocean Sampling Day activities for 2013. This workshop will extend the DwC/MIxS integration workshop from February, 2012 and the Semantics of Biodiversity Workshop from May, 2012.

The second hackathon will happen on Friday the 21st and will be hosted in conjunction with MicroB3, focusing on Field Information Management Systems, including:

  • A format for common data validation. 
  • Getting applications to adopt minimum standards (MCI, MISC, etc...) and exploring common APIs etc..
  • GUID assignment --- developing common/expected formats and standards for identifiers 
  • Exchange formats (e.g MIxS profile from GBIF, others) for rapid publication to various sources (GBIF, NCBI, BOLD, GOLD, etc...) 
  • Defining Webservice endpoints for data synchronisation among FIMS

Tuesday 12 June 2012

Geneious Challenge at iEVOBIO - plugins to be donated to Biocode Commons


2012 Geneious Challenge

Evolutionary research has many tools with many interfaces and many parameters. Learning each new tool can be tiresome, so putting as many tools as possible into a single platform with a single learning curve makes a lot of sense.
In 2012, Biomatters is sponsoring a new challenge as part of iEvoBio. The 2012 Geneious Challenge will run in parallel to the iEvoBio Challenge and we're challenging you to create any new feature, analysis or visualization as a plugin to Geneious Pro that meets our basic criterion - it has to be awesome. Using our Public API, you could wrap an existing algorithm alignment, assembly or phylogenetic algorithm, build a massive treeviewer for phylogenies with 1000+ taxa, implement a tree comparison algorithm, develop a cool way to display multiple trees in three dimensions, dare to be different and visualize a circular sequence alignment, contig scaffold viewer for NGS data, or simply application or web-service to provide something novel to the Geneious platform - we don't care! It just has to be awesome!
$1000 cash prize will be awarded for first place and 12-month subscription licenses for Geneious Pro will be provided to all entrants that submit their plugin before June 25, 2012 for judging*. The winning entries will be selected by a vote of the iEvoBio meeting participants. Meeting participants will be asked to vote for the entry which makes the most substantial novel contribution, so each entry must be easily recognizable as a distinct contribution from the previously existing architecture of Geneious Pro.
Plugin entries have no requirement to be recently published or unpublished, but must be open-source software that is released either under the LGPL 2.0+ or similar, so that Biomatters can donate the plugins to the Biocode Commons, a freeware initiative that will allow others to build on your code.

Monday 11 June 2012

Biocode Commons website updated and Blog Launched

The Biocode Commons website was updated after the "Moorea Genomic Observatory" meeting (Moorea June 1-5, 2012).  A blog to accompany the main website has now also been launched.

Biocode Commons homepage: http://biocodecommons.org/