Bioinformatics Open Source Conference (#BOSC2013) at Berlin

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.

BIOINFORMATICS OPEN SOURCE CONFERENCE 2013, DAY 1 MORNING: CAMERON NEYLON AND OPEN SCIENCE

Covers -

NETWORK READY RESEARCH: THE ROLE OF OPEN SOURCE AND OPEN THINKING

Cameron Neylon

OPEN SCIENCE DATA FRAMEWORK: A CLOUD ENABLED SYSTEM TO STORE, ACCESS, AND ANALYZE SCIENTIFIC DATA

Anup Mahurkar

MYEXPERIMENT RESEARCH OBJECTS: BEYOND WORKFLOWS AND PACKS

Stian Soiland-Reyes

EMPOWERING CANCER RESEARCH THROUGH OPEN DEVELOPMENT

Juli Klemm

DNADIGEST A NOT-FOR-PROFIT ORGANISATION TO PROMOTE AND ENABLE OPEN-ACCESS SHARING OF GENOMICS DATA

Fiona Nielsen

JUG: REPRODUCIBLE RESEARCH IN PYTHON

Luis Pedro Coelho

OPENLABFRAMEWORK: A NEXT-GENERATION OPEN-SOURCE LABORATORY INFORMATION MANAGEMENT SYSTEM FOR EFFICIENT SAMPLE TRACKING

Markus List

BIOINFORMATICS OPEN SOURCE CONFERENCE 2013, DAY 1 AFTERNOON: VISUALIZATION AND PROJECT UPDATES

REFINERY PLATFORM INTEGRATING VISUALIZATION AND ANALYSIS OF LARGE-SCALE BIOLOGICAL DATA

Nils Gehlenborg

DGE-VIS: VISUALISATION OF RNA-SEQ DATA FOR DIFFERENTIAL GENE EXPRESSION ANALYSIS

David Powell

GENOMIC VISUALIZATION EVERYWHERE WITH DALLIANCE

Thomas Down

ROBUST QUALITY CONTROL OF NEXT GENERATION SEQUENCING ALIGNMENT DATA

Konstantin Okonechnikov

VISUALIZING BACTERIAL SEQUENCING DATA WITH GENOMEVIEW

Thomas Abeel

GENOMICS APPLICATIONS IN THE CLOUD WITH DNANEXUS

Andrey Kislyuk

BIORUBY PROJECT UPDATES POWER OF MODULARITY IN THE COMMUNITY-BASED OPEN SOURCE DEVELOPMENT MODEL

Toshiaki Katayama

BIOPYTHON PROJECT UPDATE

Peter Cock

INTERMINE COLLABORATIVE DATA MINING

Alex Kalderimis

THE GENOCAD 2.2 GRAMMAR EDITOR

Jean Peccoud

IMPROVEMENTS AND NEW FEATURES IN THE 7TH MAJOR RELEASE OF THE BIO-LINUX DISTRO

Tim Booth

BIOINFORMATICS OPEN SOURCE CONFERENCE 2013, DAY 2 MORNING: SEAN EDDY AND SOFTWARE INTEROPERABILITY

**BIOLOGICAL SEQUENCE ANALYSIS IN THE POST-DATA ERA

Sean Eddy**

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

Enis Afgan

TAVERNA COMPONENTS: SEMANTICALLY ANNOTATED AND SHAREABLE UNITS OF FUNCTIONALITY

Donal Fellows

UGENE WORKFLOW DESIGNER ?? FLEXIBLE CONTROL AND EXTENSION OF PIPELINES WITH SCRIPTS

Yuriy Vaskin

REPRODUCIBLE QUANTITATIVE TRANSCRIPTOME ANALYSIS WITH OQTANS

Vipin Sreedharan

METASEE: AN INTERACTIVE VISUALIZATION TOOLBOX FOR METAGENOMIC SAMPLE ANALYSIS AND COMPARISON

Xiaoquan Su

PHYLOCOMMONS: COMMUNITY STORAGE, ANNOTATION AND REUSE OF PHYLOGENIES

Hilmar Lapp

GEMBASSY: AN EMBOSS ASSOCIATED PACKAGE FOR GENOME ANALYSIS USING G-LANGUAGE SOAP/REST WEB SERVICES

Hidetoshi Itaya

RUBRA FLEXIBLE DISTRIBUTED PIPELINES FOR BIOINFORMATICS

Clare Sloggett