BioHDF on the Web

During the past spring and early part of summer, we presented our initial work using HDF5 technology to make next generation DNA sequencing data management scalable. The presentations are posted on web, along with other points of interest that are listed below.

Presentations:
Presentations by Mark Welsh, and myself can be found at SciVee.
Mark presents our poster at ISMB , and I present our work at the “Sequencing, Finishing and Analysis in the Future Meeting,” in Santa Fe.

We also presented at this and last year’s BOSC meetings that were held at ISMB. The abstracts and slides can be found at:

• Slides: BOSC 2009, BOSC 2008
• Abstracts: BOSC 2009, BOSC 2008

What others are thinking:
Real time commentary on the 2009 BOSC presentation can be found at friendfeed and another post. The Fisheye Perspective considers how HDF5 fits with semantic web tools.

HDF in Bioinformatics:
Check out Fast5 for using HDF5 to store sequences and base probablities.

BioHDF in the News:
Genome Web and Bioinform articles on HDF5 or referencing HDF5 include:

• NHGRI Awards Grant to Geospiza-HDF Collaboration
• Geospiza, HDF Group Snag $1.1M NHGRI Grant to Develop Scalable Data Format for Second-gen Sequencing
• Bioinformatics Pros: Labs Should Include Data Management in All Project Plans

FinchTalk:
Links to FinchTalks about BioHDF from 2008 t0 present include:

• Next Gen Sequencing Software
• The case for HDF
• Genotyping with HDF
• BioHDF at BOSC
• Introducing BioHDF

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF.

• Part I: Introduction
• Part II: Background
• Part III: The HDF5 Advantage
• Part IV: HDF5 Benefits
• Part V: Why HDF5?

HDF Software :
You can learn more about HDF5 and get the software and tools at:

• The HDF Group site
• The BioHDF site