Those not at the conference can follow Brad Chapman’s excellent write-ups linked below. Sorry for the caps below. They are cut and pasted as in Brad Chapman’s original.
We will add the remaining links, as Brad continues with his excellent commentaries.
NETWORK READY RESEARCH: THE ROLE OF OPEN SOURCE AND OPEN THINKING
OPEN SCIENCE DATA FRAMEWORK: A CLOUD ENABLED SYSTEM TO STORE, ACCESS, AND ANALYZE SCIENTIFIC DATA
MYEXPERIMENT RESEARCH OBJECTS: BEYOND WORKFLOWS AND PACKS
EMPOWERING CANCER RESEARCH THROUGH OPEN DEVELOPMENT
DNADIGEST A NOT-FOR-PROFIT ORGANISATION TO PROMOTE AND ENABLE OPEN-ACCESS SHARING OF GENOMICS DATA
JUG: REPRODUCIBLE RESEARCH IN PYTHON
Luis Pedro Coelho
OPENLABFRAMEWORK: A NEXT-GENERATION OPEN-SOURCE LABORATORY INFORMATION MANAGEMENT SYSTEM FOR EFFICIENT SAMPLE TRACKING
REFINERY PLATFORM INTEGRATING VISUALIZATION AND ANALYSIS OF LARGE-SCALE BIOLOGICAL DATA
DGE-VIS: VISUALISATION OF RNA-SEQ DATA FOR DIFFERENTIAL GENE EXPRESSION ANALYSIS
GENOMIC VISUALIZATION EVERYWHERE WITH DALLIANCE
ROBUST QUALITY CONTROL OF NEXT GENERATION SEQUENCING ALIGNMENT DATA
VISUALIZING BACTERIAL SEQUENCING DATA WITH GENOMEVIEW
GENOMICS APPLICATIONS IN THE CLOUD WITH DNANEXUS
BIORUBY PROJECT UPDATES POWER OF MODULARITY IN THE COMMUNITY-BASED OPEN SOURCE DEVELOPMENT MODEL
BIOPYTHON PROJECT UPDATE
INTERMINE COLLABORATIVE DATA MINING
THE GENOCAD 2.2 GRAMMAR EDITOR
IMPROVEMENTS AND NEW FEATURES IN THE 7TH MAJOR RELEASE OF THE BIO-LINUX DISTRO
**BIOLOGICAL SEQUENCE ANALYSIS IN THE POST-DATA ERA
Sean Eddy’s talk seems to be the high point of the conference. Bedtools from @aaronquinlan’s got honorable mention in his talk.
It contains many useful insights such as the following one.
From this: general advice to not do incremental engineering is wrong. A lot of great work came from incremental engineering: automobiles, sequence analysis (Smith Waterman -> BLAST -> PSI-BLAST -> HMMER). Engineering is a valuable part of science. Requires insane dedication to a single problem. The truth: science rewards for how much impact you have, not how many papers you write. Arbitrage approach to science: take ideas and tools and make them usable for biologists who need them. Not traditionally valuable but useful so can carve out a niche.
BIOBLEND ENABLING PIPELINE DREAMS
TAVERNA COMPONENTS: SEMANTICALLY ANNOTATED AND SHAREABLE UNITS OF FUNCTIONALITY
UGENE WORKFLOW DESIGNER ?? FLEXIBLE CONTROL AND EXTENSION OF PIPELINES WITH SCRIPTS
REPRODUCIBLE QUANTITATIVE TRANSCRIPTOME ANALYSIS WITH OQTANS
METASEE: AN INTERACTIVE VISUALIZATION TOOLBOX FOR METAGENOMIC SAMPLE ANALYSIS AND COMPARISON
PHYLOCOMMONS: COMMUNITY STORAGE, ANNOTATION AND REUSE OF PHYLOGENIES
GEMBASSY: AN EMBOSS ASSOCIATED PACKAGE FOR GENOME ANALYSIS USING G-LANGUAGE SOAP/REST WEB SERVICES
RUBRA FLEXIBLE DISTRIBUTED PIPELINES FOR BIOINFORMATICS