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Old 02-25-2015, 03:53 AM   #1
plabaj
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Lightbulb Camda 2015

Dear Colleagues,

We announce a Call for Contributions to the CAMDA Satellite Meeting of ISMB/ECCB: Researchers world-wide take the CAMDA Challenge (www.camda.info) - compete with the best in an open-ended data analysis contest!

For 2015, the FDA SEQC consortium offers two challenges:
(i) the response of over 100 rat livers to 27 drugs representing 9 different chemical modes of action, as characterized by matched RNA-Seq and microarray expression profiles, and
(ii) a multi-site cross-platform RNA-Seq benchmark covering 3 next-generation sequencing, 5 microarray, and 2 qPCR platforms.
(You can read more about SEQC consortium outcome here: http://www.nature.com/nbt/collections/seqc/index.html)

By popular request, we also repeat the challenge of an integrated analysis of hundreds of cancer patients with matched profiles of mRNA and miRNA expression, methylation, copy number variation, and SNPs.

Join us and keynote speakers Des Higgins and Gad Getz (tbc) for a stimulating scientific meeting and lively discussions over a Guinness in Dublin 10-11 July 2015!

Please follow us on twitter @CAMDA_conf!


Background:

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 gene expression profiling. It aims to establish the state-of-the-art in analysis methods for Big Data in the Life Sciences, 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. 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 Systems Biomedicine journal (Taylor & Francis).

Running as an official Satellite meeting of ISMB/ECCB (established since 2011) provides further opportunities for interaction with colleagues.

Keynotes by leading researchers in the field provide further focus points for discussion at the meeting.

We hope to see you in Dublin!


Best Regards,

CAMDA 2015 organizing committee:
Walter Kolch, Dublin, Ireland
Joaquin Dopazo, Valencia, Spain
Lan Hu, Boston, USA
Okko Clevert, Berlin, Germany
David Kreil, Vienna, Austria​
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Old 03-30-2015, 06:38 AM   #2
datha99
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Default Help on Data Download for CAMDA 2015 Challenges

Dear plabaj,

We have been trying to download the three cancer data sets (ICGC Cancer Genome Consortium Challenges) for CAMDA 2015. However we are facing problems with download of the meth_array data set.

Please suggest on how to sort out this problem..

I've also tried contacting ICGC folks and haven't received a response yet.
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Old 03-30-2015, 07:35 AM   #3
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Dear datha99,

The problem is probably on the ICGC site, we will try to investigate this but to do so we would need more information about problems you encountered.
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Old 03-30-2015, 09:37 PM   #4
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Dear plabaj,

We were trying to download the 3 data sets for the challenge from the ICGC website.

The download problem is limited only to the methylation array data sets:

meth_array.HNSC-US.tsv.gz - (https://dcc.icgc.org/repository/rele...ojects/HNSC-US) 2.70 GB

meth_array.LUAD-US.tsv.gz - (https://dcc.icgc.org/repository/rele...ojects/LUAD-US) 2.55 GB

meth_array.KIRC-US.tsv.gz - (https://dcc.icgc.org/repository/rele...ojects/KIRC-US) 2.79 GB

The downloads commence fine and are shown to be completed after downloading approx. > 1 GB of data. However, the extraction of the the .gz files fails as incomplete files.

This problem is with all the three files specified above.

Please look into this issue.

Thank you and regards...
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Old 04-01-2015, 01:59 AM   #5
plabaj
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Dear datha99,

I can confirm that we are experiencing the same problems. We have reported the issue to the ICGC and waiting for the response.

We are sorry for these inconveniences but we do not have any influence on them.
We hope that this problem will be solved soon.
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Old 04-01-2015, 09:24 AM   #6
plabaj
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Dear datha99,

I have just verified that there are no problems with downloading data from the newer release. So please use release 18 instead of 17.

We will put an appropriate note on the CAMDA home page.
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Old 04-15-2015, 11:29 PM   #7
datha99
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Default Thank you

Dear plabaj,

Thank you for reverting back and updating the CAMDA challenge page.

ICGC folks also contacted me on this problem reported through their website.

I'll update if the problem is fixed.

Regards...
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Old 04-27-2015, 03:24 AM   #8
plabaj
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CAMDA Challange has beedn cited in PLOS Computational Biology Ten Simple Rules for a Community Computational Challenge
http://journals.plos.org/ploscompbio...l.pcbi.1004150
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Old 04-29-2015, 09:13 AM   #9
alyh
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Default Problem fixed!

Dear plabaj and datha99,

We have just added support for HTTP Range headers to fix the issues you were facing. This means that the download will pickup from where it last stopped in the case that it fails. You can download the files you were trying to get using the following:

HNSC-US methylation array data
Code:
wget -c -t 0 https://dcc.icgc.org/api/v1/download?fn=/release_18/Projects/HNSC-US/meth_array.HNSC-US.tsv.gz
LUAD-US methylation array data
Code:
wget -c -t 0 https://dcc.icgc.org/api/v1/download?fn=/release_17/Projects/LUAD-US/meth_array.LUAD-US.tsv.gz
KIRC-US methylation array data
Code:
wget -c -t 0 https://dcc.icgc.org/api/v1/download?fn=/release_17/Projects/KIRC-US/meth_array.KIRC-US.tsv.gz
Please refer to this link (http://www.cyberciti.biz/tips/wget-r...-download.html) for more information about continuing downloads.

Thanks
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Old 05-04-2015, 01:14 AM   #10
plabaj
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Lightbulb Keynote Speaker: Christopher E. Mason, PhD

It is a great pleasure to announce that in addition to

Prof. Des Higgins

the keynote speaker at CAMDA 2015 will be

Prof. Christopher E. Mason

Prof. Mason is known from the management & leading roles in SEQC and ABRF consortia (http://www.nature.com/nbt/collections/seqc/index.html) as well as the recent involvement in PhatoMap project or NASA twin study.

Short Bio: Christopher E. Mason completed his dual B.S. in Genetics and Biochemistry from University of Wisconsin-Madison in 2001, his Ph.D. in Genetics from Yale University in 2006, and his post-doctoral training at Yale Medical School, while also holding a fellowship at Yale Law School. In 2009, Dr. Mason founded his laboratory as an assistant professor at Weill Cornell Medical College in the Department of Physiology and Biophysics and at the Institute for Computational Biomedicine. Professor Mason also holds an appointment in the Tri-Institutional Program on Computational Biology and Medicine between Cornell, Memorial Sloan-Kettering Cancer Center and Rockefeller University and he also has an appointment at the Weill Cornell Cancer Center and the Brain and Mind Research Institute. In 2013, he won the Hirschl-Weill-Caulier Career Scientist Award. In 2014, he won the Vallee Foundation Young Investigator Award, the CDC Honor Award for Standardization of Clinical Testing, and he was just named as one of the “Brilliant Ten” Scientists in the world by Popular Science magazine. In 2015, he became the first WorldQuant Foundation Research Scholar, was recently promoted to associate professor, and his work has been featured across the world in over 300 media outlets.
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