CAMDA 2017 at ISMB/ECCB

plabaj · 12-22-2016, 09:00 AM

Dear Colleagues,

The Call for Contributions to CAMDA is now open!

CAMDA is a full conference track at ISMB (www.camda.info).

Researchers world-wide take the CAMDA Challenge (contest.camda.info) - compete with the best in an open-ended data analysis contest!

Your choice of challenges 2017:
* The MetaSUB Challenge presents the urban microbiomes of three cities. Compare organism fingerprints from public places across cities. Investigate organism sequences and biodiversity vs location.
* The Neuroblastoma Data Integration Challenge presents clinical data, RNA-seq and Agilent gene expression, and CNV/SNP info from aCGH. Improve the prediction of clinical outcome, survival time, or disease mechanisms vs the original expression-only study by the FDA SEQC.
* The Oxford Nanopore ‘Wiggle Space’ Challenge presents raw data from one of the latest next-next-generation sequencing platforms. Calibrate reads vs matched results from established platforms. Test your interpretation of metagenomics analyses on a 'mystery' sample of patient microbiota.

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

For the organizing committee,
Joaquin Dopazo, Valencia, Spain
David Kreil, Vienna, Austria
Paweł Łabaj, Vienna, Austria

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).

Selected contributions are presented though talks and posters. Results and methods of the different analyses are discussed and compared at the conference, with delegates voting for the best presentations. Extended papers are published in a special issue of Biology Direct (fully indexed and open access). Methods papers are eligible for the regular ISMB proceedings track in Bioinformatics.

Keynotes by leading researchers in the field provide further focus points for discussion at the meeting, and have recently included talks by Atul Butte and Sandrine Dudoit (Stanford), Mark Gerstein (Yale), Curtis Huttenhower (Harvard), John Quackenbush (Dana Farber Cancer Institute, Boston), Chris Sander (Memorial Sloan Kettering Cancer Center, New York), Eran Segal (Weizmann Institute, Israel), John Storey and Olga Troyanskaya (Princeton), and Terry Speed (Berkeley & WEHI).

plabaj · 01-04-2017, 01:44 PM

Founded in 2015, the MetaSUB International Consortium aims to create the world's only longitudinal metagenomic map of mass-transit systems and other public spaces across the globe. While Global City Sampling Day covered over 40 locations, the consortium has partnered with CAMDA for the first-ever multi-city analysis, with an early release of New York City, Boston, and Sacramento exclusive to MetaSUB and CAMDA.

Analysis suggestions:

Biological: Compare organism fingerprints from public places across cities. Investigate organism sequences and biodiversity vs location. How diverse is each city – in terms of the numbers of bacteria, eukaryotes, viruses, plasmids, and antimicrobial resistance markers (AMRs)? Can we determine if each city has a distinct AMR profile?
Technical: Which computational tools have the highest sensitivity and specificity for species detection?

Check also other challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 01-11-2017, 01:50 PM

Examine the power of data integration in a real-world clinical setting. Neuroblastoma is the most common extracranial solid tumor in children. The base study compared RNA-seq and Agilent microarray gene expression profiles for clinical endpoint prediction of 498 children patients (FDA SEQC - Zhang et al, Genome Biology 2015). The published summary data are complemented by raw signal level data for gene expression arrays, RNA-Seq expression profiles, and extended clinical meta-data (event-free & overall survival times, multiple prognostic markers, therapy data). For this challenge, we newly provide matched aCGH data for 145 of these patients for CNV and SNP analysis (Fischer lab, Köln).

Analysis suggestions:

Technical: Efficient data integration, both inter-type – gene expression, CNV, SNPs – and intra-type – combining the expression profiles from complementary high-throughput technologies (RNA-seq and microarrays).
Biological: Better survival time prediction by effective data integration or improved models including alternative gene transcripts. Advance our understanding of the mechanisms behind cancer progression or therapy response by effective data integration, a first comprehensive transcript level analysis, or novel functional (network/pathway) analysis.

Check also other CAMDA challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 01-18-2017, 07:33 AM

Several gut microbiota samples had their DNA sequenced both by Nanopore long read next-next-generation sequencing as well as more established Illumina sequencing technology (Mason lab, New York, original unpublished data). Additional ‘mystery’ samples provide an independent blind test.

Questions of interest include, but are not limited to

Technical: Improve base-calling, assembly, and signal level models of the Nanopore data with the reference sequences and/or Illumina sequencing serving as benchmark. We have samples with biological and samples with technical replicates.
Biological: Meta-genomics: Detection, discrimination, and abundance quantification of species. For some training samples, relative abundances are known (synthetic mixes). Sequence / functional predictive analysis of pathogenicity. And: Analysis and identification of the ‘mystery’ sample!

Check also other CAMDA challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 01-25-2017, 07:55 AM

There are two Submission Options:

Full methods research papers can be submitted to the regular ISMB Proceedings Track (note 26th of January ISMB Proceedings deadline!), specifying CAMDA as intended target audience.
Extended abstracts of late breaking methods research or analyses of the CAMDA challenge data sets can be submitted by the CAMDA submission deadline in May. Extended abstracts should include at least preliminary key results and figures. Based on the extended abstract, the scientific committee selects teams to present their work at the CAMDA conference, where updated results need to be shown.

Check CAMDA challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 03-21-2017, 09:30 AM

There is still time to take part in CAMDA challenge(s)!

Extended abstracts of late breaking methods research or analyses of the CAMDA challenge data sets can be submitted by the CAMDA submission deadline in May. Extended abstracts should include at least preliminary key results and figures. Based on the extended abstract, the scientific committee selects teams to present their work at the CAMDA conference, where updated results need to be shown.

Check CAMDA challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 04-25-2017, 04:03 AM

Last call to take part in CAMDA challenge(s)!

Check CAMDA challenges!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

plabaj · 06-01-2017, 05:10 AM

The tentative agenda of CAMDA@ISMB is already online!

Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017!

Follow us on twitter @CAMDA_conf

See you in Prague!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
2017 Workshop on Phylogenomics. 22 Jan - 4 Feb, 2017. Cesky Krumlov, Czech Republic	shandley	Events / Conferences	0	09-05-2016 01:27 PM
Camda 2016	plabaj	Events / Conferences	2	06-02-2016 05:22 AM
Camda 2015	plabaj	Events / Conferences	9	05-04-2015 01:14 AM
CAMDA'11 - ISMB Satellite Meeting, Vienna, 15-16 July 2011 -- www.camda.info	plabaj	Events / Conferences	3	08-23-2011 11:43 AM
Ismb 2008	bioinfosm	Events / Conferences	2	07-20-2008 12:51 PM

12-22-2016, 09:00 AM	#1
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	CAMDA 2017 at ISMB/ECCB Dear Colleagues, The Call for Contributions to CAMDA is now open! CAMDA is a full conference track at ISMB (www.camda.info). Researchers world-wide take the CAMDA Challenge (contest.camda.info) - compete with the best in an open-ended data analysis contest! Your choice of challenges 2017: * The MetaSUB Challenge presents the urban microbiomes of three cities. Compare organism fingerprints from public places across cities. Investigate organism sequences and biodiversity vs location. * The Neuroblastoma Data Integration Challenge presents clinical data, RNA-seq and Agilent gene expression, and CNV/SNP info from aCGH. Improve the prediction of clinical outcome, survival time, or disease mechanisms vs the original expression-only study by the FDA SEQC. * The Oxford Nanopore ‘Wiggle Space’ Challenge presents raw data from one of the latest next-next-generation sequencing platforms. Calibrate reads vs matched results from established platforms. Test your interpretation of metagenomics analyses on a 'mystery' sample of patient microbiota. Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! For the organizing committee, Joaquin Dopazo, Valencia, Spain David Kreil, Vienna, Austria Paweł Łabaj, Vienna, Austria 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). Selected contributions are presented though talks and posters. Results and methods of the different analyses are discussed and compared at the conference, with delegates voting for the best presentations. Extended papers are published in a special issue of Biology Direct (fully indexed and open access). Methods papers are eligible for the regular ISMB proceedings track in Bioinformatics. Keynotes by leading researchers in the field provide further focus points for discussion at the meeting, and have recently included talks by Atul Butte and Sandrine Dudoit (Stanford), Mark Gerstein (Yale), Curtis Huttenhower (Harvard), John Quackenbush (Dana Farber Cancer Institute, Boston), Chris Sander (Memorial Sloan Kettering Cancer Center, New York), Eran Segal (Weizmann Institute, Israel), John Storey and Olga Troyanskaya (Princeton), and Terry Speed (Berkeley & WEHI). __________________ Pawel Labaj

01-04-2017, 01:44 PM	#2
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	MetaSUB Inter-City Challenge Founded in 2015, the MetaSUB International Consortium aims to create the world's only longitudinal metagenomic map of mass-transit systems and other public spaces across the globe. While Global City Sampling Day covered over 40 locations, the consortium has partnered with CAMDA for the first-ever multi-city analysis, with an early release of New York City, Boston, and Sacramento exclusive to MetaSUB and CAMDA. Analysis suggestions: Biological: Compare organism fingerprints from public places across cities. Investigate organism sequences and biodiversity vs location. How diverse is each city – in terms of the numbers of bacteria, eukaryotes, viruses, plasmids, and antimicrobial resistance markers (AMRs)? Can we determine if each city has a distinct AMR profile? Technical: Which computational tools have the highest sensitivity and specificity for species detection? Check also other challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

01-11-2017, 01:50 PM	#3
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Neuroblastoma Data Integration Challenge Examine the power of data integration in a real-world clinical setting. Neuroblastoma is the most common extracranial solid tumor in children. The base study compared RNA-seq and Agilent microarray gene expression profiles for clinical endpoint prediction of 498 children patients (FDA SEQC - Zhang et al, Genome Biology 2015). The published summary data are complemented by raw signal level data for gene expression arrays, RNA-Seq expression profiles, and extended clinical meta-data (event-free & overall survival times, multiple prognostic markers, therapy data). For this challenge, we newly provide matched aCGH data for 145 of these patients for CNV and SNP analysis (Fischer lab, Köln). Analysis suggestions: Technical: Efficient data integration, both inter-type – gene expression, CNV, SNPs – and intra-type – combining the expression profiles from complementary high-throughput technologies (RNA-seq and microarrays). Biological: Better survival time prediction by effective data integration or improved models including alternative gene transcripts. Advance our understanding of the mechanisms behind cancer progression or therapy response by effective data integration, a first comprehensive transcript level analysis, or novel functional (network/pathway) analysis. Check also other CAMDA challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

01-18-2017, 07:33 AM	#4
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Oxford Nanopore ‘Wiggle Space’ Challenge Several gut microbiota samples had their DNA sequenced both by Nanopore long read next-next-generation sequencing as well as more established Illumina sequencing technology (Mason lab, New York, original unpublished data). Additional ‘mystery’ samples provide an independent blind test. Questions of interest include, but are not limited to Technical: Improve base-calling, assembly, and signal level models of the Nanopore data with the reference sequences and/or Illumina sequencing serving as benchmark. We have samples with biological and samples with technical replicates. Biological: Meta-genomics: Detection, discrimination, and abundance quantification of species. For some training samples, relative abundances are known (synthetic mixes). Sequence / functional predictive analysis of pathogenicity. And: Analysis and identification of the ‘mystery’ sample! Check also other CAMDA challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

01-25-2017, 07:55 AM	#5
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Submission options There are two Submission Options: Full methods research papers can be submitted to the regular ISMB Proceedings Track (note 26th of January ISMB Proceedings deadline!), specifying CAMDA as intended target audience. Extended abstracts of late breaking methods research or analyses of the CAMDA challenge data sets can be submitted by the CAMDA submission deadline in May. Extended abstracts should include at least preliminary key results and figures. Based on the extended abstract, the scientific committee selects teams to present their work at the CAMDA conference, where updated results need to be shown. Check CAMDA challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

03-21-2017, 09:30 AM	#6
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Still time to take part in CAMDA challenge(s) There is still time to take part in CAMDA challenge(s)! Extended abstracts of late breaking methods research or analyses of the CAMDA challenge data sets can be submitted by the CAMDA submission deadline in May. Extended abstracts should include at least preliminary key results and figures. Based on the extended abstract, the scientific committee selects teams to present their work at the CAMDA conference, where updated results need to be shown. Check CAMDA challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

04-25-2017, 04:03 AM	#7
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Last Call! Last call to take part in CAMDA challenge(s)! Check CAMDA challenges! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj

06-01-2017, 05:10 AM	#8
plabaj Member Location: Vienna Join Date: Oct 2010 Posts: 86	Tentative schedule online The tentative agenda of CAMDA@ISMB is already online! Join us for a stimulating scientific meeting and lively discussions in Prague 22-23 July 2017! Follow us on twitter @CAMDA_conf See you in Prague! __________________ Pawel Labaj