CAGI conference confirmed: 25-27 March 2016; Lead Scientist job open

Dear CAGI Participant,

* The CAGI 4 conference will be held on 25-27 March 2016 at Genentech Hall on the UCSF Mission Bay campus in San Francisco, California. Although this overlaps Good Friday and Easter Sunday, and also affects Purim, our survey indicates that most likely attendees prefer to hold the conference on these dates. The week leading up to the conference is Spring Break at many universities in the US, which is convenient for those with teaching responsibilities. We sincerely apologize to those of you who are unable to attend due to this conflict.

We will post registration and logistics information soon. We will not be having a room block, and we advise exploring AirBNB for accommodation in additional traditional hotels.

* We remind you that three CAGI 4 challenges are still open:
Bipolar exomes (closes 25 January 2016):
Distinguish between exomes of bipolar disorder patients and unaffected individuals
https://genomeinterpretation.org/content/4-bipolar-exomes

Hopkins clinical panel (closes 18 January 2016):
Predict patients’ clinical descriptions and pathogenic variants from gene panel sequences
https://genomeinterpretation.org/content/4-Hopkins_clinical_panel

SickKids clinical genomes (closes 1 February 2016):
Predict patients’ clinical descriptions and pathogenic variants from their genome sequences
https://genomeinterpretation.org/content/4-SickKids_clinical_genomes

* We are seeking a successor Lead Scientist or Postdoctoral researcher for CAGI. If you know of any outstanding candidates, please refer them to us and encourage them to apply. The initial review of applications is now underway, and we hope to move quickly to allow substantial overlap of this appointment with Roger Hoskins.
http://compbio.berkeley.edu/jobs and https://genomeinterpretation.org
Apply at
https://aprecruit.berkeley.edu/apply/JPF00954 (Scientist)
or by email to "jobs@compbio.berkeley.edu" (Postdoc)

We remind you to check the website and follow us @CAGInews for more updates.

Finally, our colleagues at CAMDA have just released three challenges. Please see details, below.

Best wishes for 2016.

Roger, John, and Steven

Call for Contributions: Critical Assessment of Massive Data Analysis
| www.camda.info | 8-9 July Orlando, Flordia ---

CAMDA was founded in 2000 (Nature 411, 885. Nature 424, 610) to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, including but not limited to high-dimensional -omics data (see www.camda.info for general background). It aims to establish the state-of-the-art in analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a community-wide contest, with the scientific community analysing the same data sets. Besides traditional classification problems, there is a regular focus on

measurement accuracy / data processing
complex integrative open ended biological inference

Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569). Accepted contributions are presented though talks and posters, and the results and methods of the different analyses are discussed and compared at the conference, with selected presentations published in a special Open Access proceedings issue in collaboration with the F1000 Research Journal, which are fully pubmed indexed.

This year's contest offers three challenges:

The Oxford Nanopore ‘wiggle space’ challenge (Mason lab, New York, original unpublished data). Several microbiota samples had their DNA sequenced by Nanopore long read next-next-generation sequencing as well as more established sequencing technology. Additional ‘mystery’ samples provide an independent blind test.
Sequencing Quality Control neuroblastoma study (SEQC, Fischer lab, Köln). A comparison of RNA-seq and Agilent microarray gene expression profiles for clinical endpoint prediction (Zhang et al, Genome Biology 2015) assessed 498 children patients. The published summary data are complemented by raw signal level data sets for sequencing and arrays, and extended clinical meta-data (event-free & overall survival times, multiple prognostic markers, therapy data). In addition, we newly provide: whole genome shotgun (WGS) data of 56 patients for both cancer tissue and normal cells (~30x coverage), and array CGH data of 200 patients (for CNV and SNP analysis).
Sequencing Quality Control toxicogenomics project (SEQC consortium) – an extension building on a contest of CAMDA 2015 for continuity. A comparison of RNA-seq and Affymetrix microarray gene expression profiles (Wang et al, Nature Biotech. 2014) assessed 27 drugs representing 7 biochemical modes, testing over 100 rat livers. Summary & raw data available. New: Rat gene models can now be extended through the RatBodyMap project, which provides RNA-seq profiles of over 300 biologically distinct samples (both sexes, 10 tissues, 4 developmental stages; Yu et al, Nature Comm. 2014).

Running as an official Satellite meeting of ISMB provides further opportunities for interaction with colleagues.

Keynotes by leading researchers in the field provide further focus points for discussion at the meeting, with both experimental and theoretical issues covered, and recent keynote speakers including Mark Gerstein, John Quackenbush, Chris Sander, Eran Segal, Temple Smith and Terry Speed.

We look forward to your contribution to an exciting meeting!