SlideShare una empresa de Scribd logo
1 de 6
Descargar para leer sin conexión
Codefest 2012

                  Brad Chapman




Bioinformatics Open Source Conference, 13 July 2012
Overview



      2 day coding session before BOSC
      3rd year
      Everyone is welcome




  http://open-bio.org/wiki/Codefest_2012
Bio-Linux packages


      Galaxy packaging
      Moving towards intelligent configuration with available tools
      + wrappers during install on Bio-Linux
      Packaged Shrimp aligner + Trinity + additional lab software
      Tim Booth, Torsten Seemann, Soon Gweon
      https:
      //launchpad.net/~nebc/+archive/galaxy/+packages
BioCloudCentral



      Easier entry page: pulls existing clusters and pre-fills
      Generalize S3 buckets: 1000 genomes + loads of data
      Eucalyptus
      SQLite deployment for local installations
      Ntino Krampis, Enis Afgan, Dannon Baker




   http://biocloudcentral.org
1000 genomes documentation




      Work with 1000 genomes data on public resources
      Full workflow: BioCloudCentral, CloudBioLinux, CloudMan,
      Galaxy, IGV
      Example of complex workflow that requires full reproducibility
      Long http://j.mp/PRO8wp and short http://j.mp/LkZxDl
      versions
      Dawei Lin, Michael Heuer, Bertrand N´ron, Aaron Pilgrim
                                          e
CloudBioLinux packages



      Versions and details for all installed software
      Reproducibility: provide fully reproducible history of versioned
      software, integrated with GitHub code
      Accessibility: make packages available on nice web page like
      http://www.biogems.info/
      Debian packages, Python libraries, R libraries, custom
      installed packages
      Herv´ M´nager, Brad Chapman
          e e

Más contenido relacionado

La actualidad más candente

Chris Swan ONUG Academy - Container Networks Tutorial
Chris Swan ONUG Academy - Container Networks TutorialChris Swan ONUG Academy - Container Networks Tutorial
Chris Swan ONUG Academy - Container Networks Tutorial
Cohesive Networks
 

La actualidad más candente (12)

Docker Networking – Running multi-host applications
Docker Networking – Running multi-host applicationsDocker Networking – Running multi-host applications
Docker Networking – Running multi-host applications
 
Bioinformatics Analysis Environment for Your Laboratory Use
Bioinformatics Analysis Environment for Your Laboratory UseBioinformatics Analysis Environment for Your Laboratory Use
Bioinformatics Analysis Environment for Your Laboratory Use
 
Chris Swan ONUG Academy - Container Networks Tutorial
Chris Swan ONUG Academy - Container Networks TutorialChris Swan ONUG Academy - Container Networks Tutorial
Chris Swan ONUG Academy - Container Networks Tutorial
 
Vagrant
VagrantVagrant
Vagrant
 
Running Docker containers on Mesos
Running Docker containers on MesosRunning Docker containers on Mesos
Running Docker containers on Mesos
 
How major changes to the IT landscape are leading to new approaches in security
How major changes to the IT landscape are leading to new approaches in securityHow major changes to the IT landscape are leading to new approaches in security
How major changes to the IT landscape are leading to new approaches in security
 
Deep Dive in Docker Overlay Networks - Laurent Bernaille - Architect, D2SI
Deep Dive in Docker Overlay Networks - Laurent Bernaille - Architect, D2SIDeep Dive in Docker Overlay Networks - Laurent Bernaille - Architect, D2SI
Deep Dive in Docker Overlay Networks - Laurent Bernaille - Architect, D2SI
 
AppSec USA 2014 talk by Chris Swan "Implications & Opportunities at the Bleed...
AppSec USA 2014 talk by Chris Swan "Implications & Opportunities at the Bleed...AppSec USA 2014 talk by Chris Swan "Implications & Opportunities at the Bleed...
AppSec USA 2014 talk by Chris Swan "Implications & Opportunities at the Bleed...
 
手把手帶你學 Docker 入門篇
手把手帶你學 Docker 入門篇手把手帶你學 Docker 入門篇
手把手帶你學 Docker 入門篇
 
Nix for Python developers
Nix for Python developersNix for Python developers
Nix for Python developers
 
Deploying NPM packages with the Nix package manager
Deploying NPM packages with the Nix package managerDeploying NPM packages with the Nix package manager
Deploying NPM packages with the Nix package manager
 
Docker^3
Docker^3Docker^3
Docker^3
 

Similar a B Chapman - Codefest BOSC2012

Desktop as a Service supporting Environmental ‘omics
Desktop as a Service supporting Environmental ‘omicsDesktop as a Service supporting Environmental ‘omics
Desktop as a Service supporting Environmental ‘omics
David Wallom
 
Cloud BioLinux S.Africa
Cloud BioLinux S.AfricaCloud BioLinux S.Africa
Cloud BioLinux S.Africa
Ntino Krampis
 

Similar a B Chapman - Codefest BOSC2012 (20)

Desktop as a Service supporting Environmental ‘omics
Desktop as a Service supporting Environmental ‘omicsDesktop as a Service supporting Environmental ‘omics
Desktop as a Service supporting Environmental ‘omics
 
Containers for sensor web services, applications and research @ Sensor Web Co...
Containers for sensor web services, applications and research @ Sensor Web Co...Containers for sensor web services, applications and research @ Sensor Web Co...
Containers for sensor web services, applications and research @ Sensor Web Co...
 
Cloud BioLinux S.Africa
Cloud BioLinux S.AfricaCloud BioLinux S.Africa
Cloud BioLinux S.Africa
 
Cloud computing and bioinformatics
Cloud computing and bioinformaticsCloud computing and bioinformatics
Cloud computing and bioinformatics
 
Bosc2011 ntino-krampis-full
Bosc2011 ntino-krampis-fullBosc2011 ntino-krampis-full
Bosc2011 ntino-krampis-full
 
Understanding Kubernetes
Understanding KubernetesUnderstanding Kubernetes
Understanding Kubernetes
 
Docker training
Docker trainingDocker training
Docker training
 
Containers - Portable, repeatable user-oriented application delivery. Build, ...
Containers - Portable, repeatable user-oriented application delivery. Build, ...Containers - Portable, repeatable user-oriented application delivery. Build, ...
Containers - Portable, repeatable user-oriented application delivery. Build, ...
 
Why everyone is excited about Docker (and you should too...) - Carlo Bonamic...
Why everyone is excited about Docker (and you should too...) -  Carlo Bonamic...Why everyone is excited about Docker (and you should too...) -  Carlo Bonamic...
Why everyone is excited about Docker (and you should too...) - Carlo Bonamic...
 
Moby Open Source Summit North America 2017
Moby Open Source Summit North America 2017Moby Open Source Summit North America 2017
Moby Open Source Summit North America 2017
 
F02-Cloud-Cloud BioLinux
F02-Cloud-Cloud BioLinuxF02-Cloud-Cloud BioLinux
F02-Cloud-Cloud BioLinux
 
codemotion-docker-2014
codemotion-docker-2014codemotion-docker-2014
codemotion-docker-2014
 
Reproducible bioinformatics pipelines with Docker and Anduril
Reproducible bioinformatics pipelines with Docker and AndurilReproducible bioinformatics pipelines with Docker and Anduril
Reproducible bioinformatics pipelines with Docker and Anduril
 
Prometheus
PrometheusPrometheus
Prometheus
 
Prometheus
PrometheusPrometheus
Prometheus
 
BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity...
BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity...BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity...
BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity...
 
Ntino Krampis GSC 2011
Ntino Krampis GSC 2011Ntino Krampis GSC 2011
Ntino Krampis GSC 2011
 
Developing an open source community for cloud bioinformatics
Developing an open source community for cloud bioinformaticsDeveloping an open source community for cloud bioinformatics
Developing an open source community for cloud bioinformatics
 
Docker Azure Friday OSS March 2017 - Developing and deploying Java & Linux on...
Docker Azure Friday OSS March 2017 - Developing and deploying Java & Linux on...Docker Azure Friday OSS March 2017 - Developing and deploying Java & Linux on...
Docker Azure Friday OSS March 2017 - Developing and deploying Java & Linux on...
 
Docker en kernel security
Docker en kernel securityDocker en kernel security
Docker en kernel security
 

Más de Jan Aerts

Visual Analytics in Omics - why, what, how?
Visual Analytics in Omics - why, what, how?Visual Analytics in Omics - why, what, how?
Visual Analytics in Omics - why, what, how?
Jan Aerts
 
Visual Analytics talk at ISMB2013
Visual Analytics talk at ISMB2013Visual Analytics talk at ISMB2013
Visual Analytics talk at ISMB2013
Jan Aerts
 
Visualizing the Structural Variome (VMLS-Eurovis 2013)
Visualizing the Structural Variome (VMLS-Eurovis 2013)Visualizing the Structural Variome (VMLS-Eurovis 2013)
Visualizing the Structural Variome (VMLS-Eurovis 2013)
Jan Aerts
 

Más de Jan Aerts (20)

VIZBI 2014 - Visualizing Genomic Variation
VIZBI 2014 - Visualizing Genomic VariationVIZBI 2014 - Visualizing Genomic Variation
VIZBI 2014 - Visualizing Genomic Variation
 
Visual Analytics in Omics - why, what, how?
Visual Analytics in Omics - why, what, how?Visual Analytics in Omics - why, what, how?
Visual Analytics in Omics - why, what, how?
 
Visual Analytics in Omics: why, what, how?
Visual Analytics in Omics: why, what, how?Visual Analytics in Omics: why, what, how?
Visual Analytics in Omics: why, what, how?
 
Visual Analytics talk at ISMB2013
Visual Analytics talk at ISMB2013Visual Analytics talk at ISMB2013
Visual Analytics talk at ISMB2013
 
Visualizing the Structural Variome (VMLS-Eurovis 2013)
Visualizing the Structural Variome (VMLS-Eurovis 2013)Visualizing the Structural Variome (VMLS-Eurovis 2013)
Visualizing the Structural Variome (VMLS-Eurovis 2013)
 
Humanizing Data Analysis
Humanizing Data AnalysisHumanizing Data Analysis
Humanizing Data Analysis
 
Intro to data visualization
Intro to data visualizationIntro to data visualization
Intro to data visualization
 
L Fu - Dao: a novel programming language for bioinformatics
L Fu - Dao: a novel programming language for bioinformaticsL Fu - Dao: a novel programming language for bioinformatics
L Fu - Dao: a novel programming language for bioinformatics
 
J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module...
J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module...J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module...
J Wang - bioKepler: a comprehensive bioinformatics scientific workflow module...
 
S Cain - GMOD in the cloud
S Cain - GMOD in the cloudS Cain - GMOD in the cloud
S Cain - GMOD in the cloud
 
B Temperton - The Bioinformatics Testing Consortium
B Temperton - The Bioinformatics Testing ConsortiumB Temperton - The Bioinformatics Testing Consortium
B Temperton - The Bioinformatics Testing Consortium
 
J Goecks - The Galaxy Visual Analysis Framework
J Goecks - The Galaxy Visual Analysis FrameworkJ Goecks - The Galaxy Visual Analysis Framework
J Goecks - The Galaxy Visual Analysis Framework
 
S Cain - GMOD in the cloud
S Cain - GMOD in the cloudS Cain - GMOD in the cloud
S Cain - GMOD in the cloud
 
B Chapman - Toolkit for variation comparison and analysis
B Chapman - Toolkit for variation comparison and analysisB Chapman - Toolkit for variation comparison and analysis
B Chapman - Toolkit for variation comparison and analysis
 
P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...
P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...
P Rocca-Serra - The open source ISA metadata tracking framework: from data cu...
 
J Klein - KUPKB: sharing, connecting and exposing kidney and urinary knowledg...
J Klein - KUPKB: sharing, connecting and exposing kidney and urinary knowledg...J Klein - KUPKB: sharing, connecting and exposing kidney and urinary knowledg...
J Klein - KUPKB: sharing, connecting and exposing kidney and urinary knowledg...
 
S Cheng - eagle-i: development and expansion of a scientific resource discove...
S Cheng - eagle-i: development and expansion of a scientific resource discove...S Cheng - eagle-i: development and expansion of a scientific resource discove...
S Cheng - eagle-i: development and expansion of a scientific resource discove...
 
A Kanterakis - PyPedia: a python crowdsourcing development environment for bi...
A Kanterakis - PyPedia: a python crowdsourcing development environment for bi...A Kanterakis - PyPedia: a python crowdsourcing development environment for bi...
A Kanterakis - PyPedia: a python crowdsourcing development environment for bi...
 
A Kalderimis - InterMine: Embeddable datamining components
A Kalderimis - InterMine: Embeddable datamining componentsA Kalderimis - InterMine: Embeddable datamining components
A Kalderimis - InterMine: Embeddable datamining components
 
E Afgan - Zero to a bioinformatics analysis platform in four minutes
E Afgan - Zero to a bioinformatics analysis platform in four minutesE Afgan - Zero to a bioinformatics analysis platform in four minutes
E Afgan - Zero to a bioinformatics analysis platform in four minutes
 

Último

Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Victor Rentea
 
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
?#DUbAI#??##{{(☎️+971_581248768%)**%*]'#abortion pills for sale in dubai@
 
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers:  A Deep Dive into Serverless Spatial Data and FMECloud Frontiers:  A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Safe Software
 

Último (20)

Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024Finding Java's Hidden Performance Traps @ DevoxxUK 2024
Finding Java's Hidden Performance Traps @ DevoxxUK 2024
 
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot TakeoffStrategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
 
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemkeProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke
 
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
 
WSO2's API Vision: Unifying Control, Empowering Developers
WSO2's API Vision: Unifying Control, Empowering DevelopersWSO2's API Vision: Unifying Control, Empowering Developers
WSO2's API Vision: Unifying Control, Empowering Developers
 
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
+971581248768>> SAFE AND ORIGINAL ABORTION PILLS FOR SALE IN DUBAI AND ABUDHA...
 
Elevate Developer Efficiency & build GenAI Application with Amazon Q​
Elevate Developer Efficiency & build GenAI Application with Amazon Q​Elevate Developer Efficiency & build GenAI Application with Amazon Q​
Elevate Developer Efficiency & build GenAI Application with Amazon Q​
 
Six Myths about Ontologies: The Basics of Formal Ontology
Six Myths about Ontologies: The Basics of Formal OntologySix Myths about Ontologies: The Basics of Formal Ontology
Six Myths about Ontologies: The Basics of Formal Ontology
 
TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data DiscoveryTrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery
 
AWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of TerraformAWS Community Day CPH - Three problems of Terraform
AWS Community Day CPH - Three problems of Terraform
 
Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...
 
[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdf[BuildWithAI] Introduction to Gemini.pdf
[BuildWithAI] Introduction to Gemini.pdf
 
DBX First Quarter 2024 Investor Presentation
DBX First Quarter 2024 Investor PresentationDBX First Quarter 2024 Investor Presentation
DBX First Quarter 2024 Investor Presentation
 
Vector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptxVector Search -An Introduction in Oracle Database 23ai.pptx
Vector Search -An Introduction in Oracle Database 23ai.pptx
 
"I see eyes in my soup": How Delivery Hero implemented the safety system for ...
"I see eyes in my soup": How Delivery Hero implemented the safety system for ..."I see eyes in my soup": How Delivery Hero implemented the safety system for ...
"I see eyes in my soup": How Delivery Hero implemented the safety system for ...
 
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
Apidays New York 2024 - Passkeys: Developing APIs to enable passwordless auth...
 
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingRepurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
 
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers:  A Deep Dive into Serverless Spatial Data and FMECloud Frontiers:  A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
 
Biography Of Angeliki Cooney | Senior Vice President Life Sciences | Albany, ...
Biography Of Angeliki Cooney | Senior Vice President Life Sciences | Albany, ...Biography Of Angeliki Cooney | Senior Vice President Life Sciences | Albany, ...
Biography Of Angeliki Cooney | Senior Vice President Life Sciences | Albany, ...
 
MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024
 

B Chapman - Codefest BOSC2012

  • 1. Codefest 2012 Brad Chapman Bioinformatics Open Source Conference, 13 July 2012
  • 2. Overview 2 day coding session before BOSC 3rd year Everyone is welcome http://open-bio.org/wiki/Codefest_2012
  • 3. Bio-Linux packages Galaxy packaging Moving towards intelligent configuration with available tools + wrappers during install on Bio-Linux Packaged Shrimp aligner + Trinity + additional lab software Tim Booth, Torsten Seemann, Soon Gweon https: //launchpad.net/~nebc/+archive/galaxy/+packages
  • 4. BioCloudCentral Easier entry page: pulls existing clusters and pre-fills Generalize S3 buckets: 1000 genomes + loads of data Eucalyptus SQLite deployment for local installations Ntino Krampis, Enis Afgan, Dannon Baker http://biocloudcentral.org
  • 5. 1000 genomes documentation Work with 1000 genomes data on public resources Full workflow: BioCloudCentral, CloudBioLinux, CloudMan, Galaxy, IGV Example of complex workflow that requires full reproducibility Long http://j.mp/PRO8wp and short http://j.mp/LkZxDl versions Dawei Lin, Michael Heuer, Bertrand N´ron, Aaron Pilgrim e
  • 6. CloudBioLinux packages Versions and details for all installed software Reproducibility: provide fully reproducible history of versioned software, integrated with GitHub code Accessibility: make packages available on nice web page like http://www.biogems.info/ Debian packages, Python libraries, R libraries, custom installed packages Herv´ M´nager, Brad Chapman e e