CPHx: Roald Forsberg, Sponsored by CLC bio.

CLC Genomics Gateway

Roald Forsberg

CLC’s take on next generation of genome informatics tools.

At the 10th aniversary of the human genome project.  We now have a common and comprehensible coordinate system.. That’s a real tangible effect of the project.  So much of the work we now do is based upon this first human genome coordinate set.    HUGE list of things we can do, because of it.

However, if you look at pre-NGS work, all of the efforts were focussed on making sense of the data and annotating it – and sometimes looking at it.  It was all centralized, curated, etc.

In the post-NGS, sequencing has now been democratized.  We have access to big dataset, changing our focus to analysis, mapping, modeling. Our data resources are now many, varied, decentralized and non-curated.  A complete paradigm shift in bioinformatics focus. [my words.]

CLC has built a platform for doing this type of work.  Server based, client based, scalability, etc..  It supports the majority of genomics workflows (de novo, reseq, chip-seq, rna-seq, smrna-seq, tag-seq.)  We lack the tools for pushing further down into integrative biology.  Pathways, diagnosis, systems biology…. but there ARE no tools for doing this.

Genome browsing is no longer enough. [Thank you, I’ve been waiting for someone to say this!]

Perl IS NOT A FRAMEWORK.  [Halelujah!]

You will not get the medical community to use this technology with perl and spreadsheets.

It is time to move downstream: CLC genomics gateway.

  • an integrated framework to visualize, analyze and combine data from the same reference genome
  • seamlessly add own expreiments in an integrated manner
  • foundation for systems biology, functional genomics, etc.

Technical details

  • One data object to store and /or point to data sources
  • lazy fetching’
  • federation of data sources
  • a graphical user interface
  • completely integrated with other bioinformatics tools
  • part of the clc systems developer kit, so developers can add components and reuse existing ones without having to maintain the gui.

Enables a wide variety of tools and integrates so you can work with other tools like blast, primer design, etc.

Visualization tools:  Bring in all of your tools into one place.  [looks clean, actually.  nice.]

Federation of data: can bring in together sources like UCSC, ENsembl, your own data, flat files, etc.

Analysis types beta. Some tools for SNP comparison and annotation, Filtering snps from federated data… basically, it brings together annotations from a variety of sources and puts it all together in one place.

More analysis types to be added, including cancer biology, further advanced features.

Beta tool is out now, with new versions coming out soon.

Also, they’re hiring bioinformaticians.



2 thoughts on “CPHx: Roald Forsberg, Sponsored by CLC bio.

  1. Pingback: Copenhagenomics » Recap of Day 1 at CPHx

  2. Pingback: Copenhagenomics 2011, in review | Fejes.ca

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