1 About OMICS Group • OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the year 2007 with the sole aim of making the information on Sciences and technology ‘Open Access’, OMICS Group publishes 400 online open access scholarly journals in all aspects of Science, Engineering, Management and Technology journals. OMICS Group has been instrumental in taking the knowledge on Science & technology to the doorsteps of ordinary men and women. Research Scholars, Students, Libraries, Educational Institutions, Research centers and the industry are main stakeholders that benefitted greatly from this knowledge dissemination. OMICS Group also organizes 300 International conferences annually across the globe, where knowledge transfer takes place through debates, round table discussions, poster presentations, workshops, symposia and exhibitions.
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About OMICS Group
• OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the year 2007 with the sole aim of making the information on Sciences and technology ‘Open Access’, OMICS Group publishes 400 online open access scholarly journals in all aspects of Science, Engineering, Management and Technology journals. OMICS Group has been instrumental in taking the knowledge on Science & technology to the doorsteps of ordinary men and women. Research Scholars, Students, Libraries, Educational Institutions, Research centers and the industry are main stakeholders that benefitted greatly from this knowledge dissemination. OMICS Group also organizes 300 International conferences annually across the globe, where knowledge transfer takes place through debates, round table discussions, poster presentations, workshops, symposia and exhibitions.
OMICS Group International is a pioneer and leading science event organizer, which publishes around 400 open access journals and conducts over 300 Medical, Clinical, Engineering, Life Sciences, Phrama scientific conferences all over the globe annually with the support of more than 1000 scientific associations and 30,000 editorial board members and 3.5 million followers to its credit.
OMICS Group has organized 500 conferences, workshops and national symposiums across the major cities including San Francisco, Las Vegas, San Antonio, Omaha, Orlando, Raleigh, Santa Clara, Chicago, Philadelphia, Baltimore, United Kingdom, Valencia, Dubai, Beijing, Hyderabad, Bengaluru and Mumbai.
Network Verification Challenge(NVC)
Anita Iskandar, PhD
Philip Morris International R&D
The sbv IMPROVER project, the website and the Symposia are part of a collaborative project designed to enable scientists to learn about and contribute to the development of a new crowd sourcing method for verification of scientific data and results. The current challenges, website and biological network models were developed and are maintained as part of a collaboration with Selventa, OrangeBus and ADS. The project is funded by Philip Morris International.
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Jamboree
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Outcomes
Introduction to
sbv IMPROVER
The Network
Verification
Challenge
(NVC)
The
“bionet”
Platform
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The Network
Verification
Challenge
(NVC)
The
“bionet”
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Introduction tosbv IMPROVER
Jamboree
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Outcomes
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Develop a robust methodology that verifies systems biology-based approaches
Genomic Literature Molecular Profiles Structures
But we lack the corresponding validation tools…
We are experiencing a data overload…
Why do we need sbv IMPROVER?
The self-assessment trap: can we all be better than average?Mol Syst Biol. 2011 Oct 11;7:537. doi: 10.1038/msb.2011.70.
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Industrial Methodology for Process Verification in Research (IMProVeR): towards systems biology verification
• IMProVER has commonalities with other crowd sourcing methods
• The main concepts of IMProVER are :• to formalize rigorours tests that determine a go or no-go decision for a
systems biology research pipeline in an industrial context• to inspire the development of enhanced methodologies by community
participation• to endow the community with datasets and benchmark to provide a
means for continuous improvement in subsequent generation of builiding blocks
• Successful implementation of IMProver will enable high credibility of a research pipeline
“Industrial Methodology for Process Verification in Research (IMProVeR): towards systems biology verification”
Pablo Meyer1, Raquel Norel1, Jörg Sprengel2, Katrin Stolle3, Thomas Bonk3, Stephanie Corthesy1, Ajay Royyuru, Julia Hoeng4, Manuel Peitsch4 and Gustavo Stolovitzky1, J. Jeremy Rice1
1 IBM Computational Biology Center, Yorktown Heights, NY, USA, 2 IBM Life Sciences Division, Zurich, Switzerland, 3 Phillip Morris International Research, Cologne, Germany, 4 Phillip Morris International Research, Neuchatel, Switzerland
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Crowdsourcing in Science1994
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Heritage Provider Network Health Prize(HPN Prize)HeritageProvider NetworkThe goal of the challenge is to de velop a breakthroughalgorithm that uses available patient data to predict andprevent unnecessary hospitalizations.
Name and description ofinitiative and organisersYear
Timeline illustrating the history of life sciences crowdsourcing initiatives
sbv IMPROVER networkverification challengePMI, Selventa and IBMTo engage the scientific community to revie w, challengeaswell as make corrections to the con ventional wisdomon molecular mechanism of the respiratory s ystem.Second networkverification challenge started andrunning until 2015.
sbv IMPROVER species translation challengePMI and IBMAddressing the limitationinwhich biological events observedin rodents can be translated to humans.
Current
Crowdsourced coders take on immunologyBig DataResearchers at Har vard Medical School & Har vard Business SchoolAnalysing the genes in volved in the production of antibodiesand immune-system sentinels called T-cell receptors.
Crowdsourcing the Human MicrobiomeuBiome, a biotech outof the California Institute for QuantitativeBiosciences (QB3)uBiome is crowdsourcing the sequencing and mappingof the human microbiome.
GE’s HealthymaginationGE,KleinerPerkins Caufield& Beyers,Mohr DavidowVentures,Venrock, and MPM CapitalAn open call to action for oncology researchers,businesses, students, and healthcare inn ovators to submitideas that will accelerate inn ovation in breast cance r.
sbv IMPROVER diagnostic signature challengePMI and IBMTest and develop different approaches to classi fyingclinical samples based on geneexpression.
Children’s LeadershipAward for the ReliableInterpretation and appropriateTransmission ofYour genomic information (CLARITY)Boston Children’s HospitalTo identify best methods and practices fo r the analysis,interpretation and r eporting of individuals’ DNA sequencedata, to provide themost meaningful results to clinicians,patients and families.
2010
WikiProject Computational BiologyWikipediaAimed at improving and organising articles onComputational Biology,Bioinformatics,ComputationalSystemsBiology and related topics.
2010WikiProject Computational BiologyWikipediaAimed at improving and organising articles onComputational Biology,Bioinformatics,ComputationalSystemsBiology and related topics.
2010Critical Assessment of protein Function Annotationalgorithms (CAFA)TheAutomated Function Prediction Special Interest GroupExperiment designed to provide large-scale assessment ofcomputational methods dedicated to predicting proteinfunction.
The AssemblathonUC Davis Genome CenterOffshoots of the Genome 10K project, these contests assessstate-of-the-artmethods in the field of genome assembly.
2010
The Critical Assessment of Genome Interpretation(CAGI)Steven Brenner, computational genomicist,University of California& John Moult, computational bio logist,Universityof MarylandAn experiment to objecti vely assess computational methodsfor predicting the impacts of genomic variation.
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2013
FolditDavid Baker,biochemistryprofessorUniversityofWashingtonSeth Cooper, lead designerFoldit is an online puzzle video game about proteinfolding to help scientists sol ve “real world” problems.
2008
Dialogue for Reverse EngineeringAssessments and Methods - DREAMGustavo Stolovitzky, IBM Computational Biology CenterThe main objecti ve of DREAM is to catalyze theinteraction between theory and experiment, specifically inthe area of cellular net work inference and quantitati vemodel building.
2007
MicroArray Quality Control (MAQC): MAQC-IIFDA micro-array platform pr oviders, RNA suppliers, E PA,NIST, academic laboratories and other stakeholdersAssess the capabilities and limitations of various dataanalysis methods in developing and validating micro-arraybased predicti ve models.
2006
MicroArray Quality Control (MAQC):MAQC-IFDA micro-array platform pr oviders, RNA suppliers, E PA,NIST, academic laboratories and other stakeholders
Provides quality control (QC) tools to the micro-arraycommunity to avoid procedural failures.
2005
Critical Assessment of Information Extractionsystems in Biology (BioCreAtIvE)Personnel from CNIO, MITRE, NCBI, Int Act/MINT and EBIBioCreAtIvE compares methods and the communityassessment of scientific progress.
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TREC GenomicsTrackWilliam Hersh, National Science Foundation IT ProgrammeA workshop for evaluating systems for informationretrieval and related technologies in the genomics domain.
2003-
2007
Critical Assessment of PRediction of Interactions(CAPRI)A management team formed of EMBL/EBI-PDBe GroupA blind prediction experiment whereby participantpredictor groups are gi ven the atomic coordinates of t woproteins that make biologically rele vant interactions.
2001
CriticalAssessmentof Massive Data Analysis (CAMDA)Simon Lin and Kimberly Johnson from theDuke University Bioinformatics Shared Resource
Founded to provide a forum to critically assess differenttechniques used in micro-array data mining.
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Knowledge Discovery and Datamining Cup(KDD Cup)Association for Computing Machinery's Special InterestGroup (ACMSIG)
The annual competition for Knowledge Disc overy andData Mining.
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2010
Critical Assessment of Protein StructurePrediction - CASP*John Moult, Uni versity of Maryland Biotechnology Institute
MicroArray Quality Control (MAQC): MAQC-IIFDA micro-array platform pr oviders, RNA suppliers, E PA,NIST, academic laboratories and other stakeholdersAssess the capabilities and limitations of various dataanalysis methods in developing and validating micro-arraybased predicti ve models.
Critical Assessment of Protein StructurePrediction - CASP*John Moult, Uni versity of Maryland Biotechnology InstituteCASP is a community-wide, worldwide experiment forprotein structure prediction taking place e very two years.
MicroArray Quality Control (MAQC):MAQC-IFDA micro-array platform pr oviders, RNA suppliers, E PA,NIST, academic laboratories and other stakeholders
Provides quality control (QC) tools to the micro-arraycommunity to avoid procedural failures.
sbv IMPROVER networkverification challengePMI, Selventa and IBMTo engage the scientific community to revie w, challengeaswell as make corrections to the con ventional wisdomon molecular mechanism of the respiratory s ystem.Second network verification challenge started andrunning until 2015.
sbv IMPROVER species translation challengePMI and IBM
Addressing the limitation inwhich biological events observedin rodents can be translated to humans.
sbv IMPROVER diagnostic signature challengePMI and IBMTest and develop different approaches to classi fyingclinical samples based on geneexpression.
Critical Assessment of Information Extractionsystems in Biology (BioCreAtIvE)Personnel from CNIO, MITRE, NCBI, Int Act/MINT and EBIBioCreAtIvE compares methods and the communityassessment of scientific progress.
Dialogue for Reverse EngineeringAssessments and Methods - DREAMGustavo Stolovitzky, IBM Computational Biology CenterThe main objecti ve of DREAM is to catalyze theinteraction between theory and experiment, specifically inthe area of cellular net work inference and quantitati vemodel building.
2007
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2004 & 2006
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20072012
20132013 - present
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sbv IMPROVER Challenges
2013 2014 2015Q1 Q2 Q4Q3 Q1 Q2 Q4Q3
Future Challenges: Being planned
Benchmarking Open
2012
Network verification: Verify and enhance pulmonary biological network models
NVC 2NVC1
Open
Species translation: Accuracy and limitations of rodent models for human diseases
Rat Human Predict human impact and then validates with human data
Predict human impact and then validates with human data
Rat cellular model
Rat cellular model
Human cellular model
Human cellular model
Concept of « Translatabillity »
Diagnostic Signature: Best analytical approaches to predicting phenotype from gene expression data
CHALLENGE
Many Phenotype prediction algorithms
Many Phenotype prediction algorithms
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+ScoringPhenotype prediction performance
Corresponding phenotype (known but not given)
Gene expression data (given)
Publicly available data: phenotype, gene expression, prior knowledge of the disease (given)
Networks Were Built Using Literature and Human Transcriptomic Data
PubMed
GSE 18341GSE 18341 LPS
Tissue StimulusData SetWhole
lung
GSE 2322GSE 2322EndotoxinLung
neutrophil
Backward Reasoning is used to infer active mechanisms from transcriptomic data to enhance the literature modelCatlett NL, et al. (2013). BMC Bioinformatics, 14, 340.
catof(CYP1A1)
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Network Models are Constructed with Nodes and Referenced Edges using BEL
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Literature Reference:
“T-bet (TBX21) transfection also induced…CXCR3 expression on human TH2 cells”
Quotation:
TBX21 transcriptional activity increases CXCR3 protein abundanceEdge:
Context: Human TH2 cell
To learn more, watch the videos/webinars: https://sbvimprover.com/challenge-3/tutorials
(Biological Expression Language)
The networks are supported by thousands of peer-reviewed scientific
The sbv IMPROVER project team (2013). On Crowd-verification of Biological Networks. Bioinformatics and Biology Insights 2013:7 307-325.
Steps in the sbv IMPROVER Network Verification Challenge
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NVC2: Continue to Refine Networks Using the Crowd
Vote on evidence, create new edges, add missing nodes
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Why should you participate?
• Gain access to high quality and novel data
• Enhance your visibility and gain recognition
• Engage with peers to advance the field
• Being invited to the Jamboree
NVC2:
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NVC2 Important Dates
Feb 2014 Jul 2014 Sept 2014 Dec 2014 Apr 2015 Mid-2015
Open Phase Jamboree Activities
Today:NVC2 Started
Network Dissemination
NVC2 Open Phase Ends
Best Performer Invitation and
Jamboree Preparation
• Attend the European Conference on Computational Biology (ECCB) workshop Sunday Sept 7 in Strasbourg, France to learn about and discuss crowd engagement methods to advance research (W13 - sbv IMPROVER Workshop)
Advantage IntegralBiomedical Research Foundation of the Academy of Athens
Boston College
Cambridge Cell Networks Ltd
Clinical Research ManagementCSIR-Institue of Microbial Technology
DSHS
Edward Sanders Scientific Consulting
ETH
Fraunhofer (SCAI)
Glenmark Pharma SA
Harvard University
Hubrecht Institute
IBCH
IBM
Kuban State University of Physical Education, Sport and Tourism
National Institutes of Health
Nestlé Institute of Health Sciences
Pablo de Olavide University
Philip Morris International
SBI
Selventa
SIB Swiss Institute of Bioinformatics
Solar Turbines, Inc.
Systems Bioengineering Group - National Technical University of Athens
University of Cincinnati
University of Louisville
University of Luxembourg
University of Perugia
University of Toledo
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The sbv IMPROVER project, the website and the Symposia are part of a collaborative project designed to enable scientists to learn about and contribute to the development of a new crowd sourcing method for verification of scientific data and results. The current challenges, website and biological network models were developed and are maintained as part of a collaboration with Selventa, OrangeBus and ADS. The project is funded by Philip Morris International.
Thank You
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Let Us Meet Again
We welcome you all to our future conferences of OMICS Group International
