RapidMiner — machine learning for the rest of us

All are welcome. Although I’ll be using examples from biology, there’s nothing bio-specific in RapidMiner, and it might be useful/interesting to geeks of other varieties too.

Experience in variant calling from exome sequencing
Francesco Lescai, Elia Stupka

Sequencing whole exomes in order to identify high penetrant variants in few individuals is becoming relatively easy, and calling variants is apparently an easy push-one-button procedure. However, understanding data quality and filtering out potential false positives in SNP calling is far more difficult. We will give a tour among the key QC and filtering issues, and discuss our experiences in calling variants from exome sequencing projects at UCL Genomics.

Analysing sequencing data on the NGS Cloud
Caroline Johnston, Matteo Turilli

The generation of large next-generation sequencing datasets is rapidly becoming a standard procedure in biology, but the resulting data requires compute resources beyond those normally available in a lab. The National Grid Service’s prototype Cloud is a first step towards a non-commercial, scalable solution for UK researchers. We will give a brief introduction to the NGS and to the Cloud prototype and will run a demo to process some short read data.

AQuA-NGS: A Quality Assessment Tool for Next Generation Sequencing Data
Zabeen Patel

The recent advancement of high-throughput sequencing enables the experimentalist to generate huge amounts of data at the genomic, transcriptomic, and epigenetic levels. However, as this is a relatively new technology, the methods for assessing the quality of the data are still limited. The AQuA-NGS system was developed as a platform-independent, desktop application for the viewing of quality assessment metrics generated by the R/Bioconductor package, ShortRead. These metrics are stored in a MySQL database, together with run and sample metadata. Using the flash-based GUI, the Bioinformatician may submit new data, browse the database, view metrics via interactive tables and charts, and directly compare QA metrics across samples, on the basis of multiple criteria. The system in its present, foundational state can perform the basic functions of generating, viewing, and comparing a limited set of QA metrics generated from Illumina/Solexa export files. It requires additional development to make it ready for public release, such as the ability to process non-Solexa files, and work with remote destinations. Once complete, it will hopefully be incorporated into the pre-processing pipeline of multiple next generation sequencing platforms.

Head for the Flowers Building, room G47A for 18:00 [map ref 31]. There’ll be drinks in the lovely Eastside Bar afterwards [map ref 19]. Campus map (PDF)

We’re looking for another speaker. If you want to do an informal talk on a topic to do with bioinformatics, genomics, or any practical tech subject that might be of interest to biogeeks — cloud computing, big data management, machine learning, development tools, algorithm tuning etc. etc. etc. — then give me a shout.

Talks are normally 20-30mins but that’s negotiable.

See here for examples of previous meets, to get an idea of what we’re about.

We have a special guest this month, Cameron Neylon, with an open-science-themed talk entitled “What have the public done for us?” Plus lightning talks on various subjects.

In other news, I’ve moved the blog over to the much cleaner and airier Barthelme theme. Drop a comment if it gives you any problems.

This month’s speakers:

Catherine Canevet — Ondex: Data integration and visualisation

Christopher Barnes — ABC-SysBio: Approximate Bayesian Computation in Python with GPU support

N. Purswani, L. Tweedy, Z. Patel, C. Suriel-Melchor — DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries

Does anyone have a link for DASbrick?

Drinks afterwards at Imperial’s Eastside Bar. See the BioGeeks blog for full details.

The distribution of votes across the parties correlates very badly with the distribution of seats they get in return.

It’s possible, and not uncommon, for a party’s overall vote share to go down and yet its parliamentary influence to go up, or vice versa.

After years of adversarial flip-flopping, the system’s thrown up a result which nobody seems to be satisfied with, regardless of their party affiliation. (Except maybe the Greens :-) )

There are electoral reform demonstrations happening tomorrow, in London and all across the country:

http://www.takebackparliament.com/

If you can spare a few hours to go along, hopefully we can get a good turnout and make the case for real change while it’s still very topical — not the waffly kind of change that politicians promise every time and never deliver.

I’ll be in Trafalgar Square from 2pm.

Andrew.

We have talks from…

Alison Cuff, UCL

The CATH database — Structural Diversity and the Question of the Fold Continuum

Andrew Martin, UCL

SAPTF — Sequence Analysis Plugin Tool Framework

John Pinney, Imperial College

GLASS — Gene LAyout by Semantic Similarity

Followed by drinks at 7:30-ish at the College Arms.

Full details, maps, directions etc. are on the BioGeeks blog.

The EMBRACE-ENFIN workshop on Expression, Interactions, and System Level Modeling

Helsinki, 5th-6th October 2009

1. Data Integration in the Life Sciences (DILS 2009) in Manchester next month, with a poster and abstract about FuncNet.

2. EMBL-EBI/ENFIN 2009 annual forum for small-medium enterprises (SMEs), in Vienna in September, with a half-hour talk on the same subject.

No ISMB for me this year, not economically justifiable without a speaking spot.

Andrew.