At ISMB, the Galaxy guys were talking about using Galaxy as an interface for analysing NGS data. I’m having a go at getting it up and running on EC2. Notes are really for my own reference, but I thought I’d post them in case they were of use to anyone else.
AWS Setup
Obviously, you need an [...]
Duygu Ucar
background about TFs. ChIPchip, ChIPseq can define binding (with noise), but knowing when binding is functional is less well characterized.
TF binding should be inferred from diverse and complimentary data.
Binding doesn’t imply functionality. Binding and gene regulation are context dependant.
Functional vs Non-functional discrimination? Which factors determine functionality of binding?
Yeast data.
Define binding::
ChIPchip (pvals [...]
Contextualise data with metadata
Only considering metadata – actual data is just in native format and linked to metadata.
Consistent reporting of metadata:
Define scope and minimal info (MIBBI http://mibbi.org), syntax (ISATAB) and semantics (OBO)
http://www.mibbi.org/index.php/Main_Page
http://isatab.sourceforge.net/
http://www.obofoundry.org/
isacreator – standalone java app to annotate and link data on the basis of community-defined metadata ontologies.
poster c19
Improvements to framework. Better input validation etc.
advanced results analysis and rendering.
data model shared by all analysis tools within a category
standard web interface www.ebi.ac.uk/Tools/category/tool
similarly SOAP API: Tools/services/soap/tool?wsdl
REST API: Tools/services/rest/tool
Soap WS GetParameters(), GetParameterDetails()
REST WS GET /parameters
[...]
Janet Thornton
Disclaimer: My notes. Fairly incoherent and probably not accurate
ELIXIR is a European effort to co-ordinate the infrastructure. Preparatory project – 10-20yr roadmap for infrastructure devel to support research.
EU 32 partners, 13 member states. 4.5mill E funding to define scope, cost of infrastructure.
Goals:
Co-ordinated data resources, integration & interoperability of data, links [...]
Matias Piipari
http://www.sanger.ac.uk/software/nmica
scalable. 1000s sequences. 100s motifs highly parallel. extendable
Actually, looking at metamotifs and motif classification in this talk.
Different TF families have different modes of binding.
Can build a metamotif that encodes the distribution across a number of motifs in a family. Like a PWM, but with confidence intervals. Developed a nested sampler to learn these from [...]
Perl cis-reg motif discovery perl mods. For designing synthetic promoters. Motifs built from promoter proximal sequences in plants. Didn’t pay attention to the actual algorithm, but see: http://seeder.agrenv.mcgill.ca. On CPAN.
Spoke to a guy working on bioHDF (GeoSpiza) over lunch. Missed his talk yesterday. Alternative to SAMtools BAM format. HDF has been around for a long while, they’ve stuck a Bio layer on top of it. Plan is to biolib-ify it to get Bio-perl |java|python|condutor) integration. Might be worth thinking about for the Gbrowse2 display [...]
Lightning talk
Steffan Moller
Debian-Med
recent needs placed on distros: high performance computing, cloud/grid – bootable images with customisations. exact spec of software and env.
increased focus on: libraries – distributing software, data management – using software
debian-med.alioth.debian.org
medical and bioinfo packages. svn package maintenance. Open community
Extension of Deb, not a split.
All packages autobuild from source for > 10 arch
Packages auto-forwarded [...]
generic C/C++ libraries for Bio::* projects. esp for data IO/parsing/interpretation
In <language of choice> bind <generic C implementation> using SWIG with Biolib
Limited pool of bioinf programmers and being spread too thin across diff language specific projects. Shared stuff good cos less duplication, more people testing code etc. Inexplicable picture of young girl. Man with beard.
Bioperl on [...]