Reproducibility:Links - Revision history

Gfursin at 13:10, 13 September 2016

2016-09-13T13:10:27Z

Gfursin: Replaced content with "Moved [https://github.com/ctuning/ck/wiki/Enabling-open-science-tools here]."

2016-09-13T13:04:12Z

Replaced content with "Moved [https://github.com/ctuning/ck/wiki/Enabling-open-science-tools here]."

Gfursin at 11:54, 27 October 2015

2015-10-27T11:54:02Z

Gfursin at 09:34, 26 October 2015

2015-10-26T09:34:11Z

Gfursin at 09:33, 26 October 2015

2015-10-26T09:33:31Z

Gfursin at 16:54, 25 October 2015

2015-10-25T16:54:06Z

Gfursin at 15:40, 24 September 2015

2015-09-24T15:40:14Z

Gfursin at 15:37, 24 September 2015

2015-09-24T15:37:01Z

Gfursin at 15:35, 24 September 2015

2015-09-24T15:35:09Z

Gfursin at 15:27, 24 September 2015

2015-09-24T15:27:24Z

← Older revision		Revision as of 13:10, 13 September 2016
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−	Moved [https://github.com/ctuning/ck/wiki/Enabling-open-science-tools ~~here~~].	+	Moved to [https://github.com/ctuning/ck/wiki/Enabling-open-science-tools GitHub].

@@ Line 1: / Line 1: @@
-[ '''''[[Reproducibility|Back to main page]]''''' ]
+Moved [https://github.com/ctuning/ck/wiki/Enabling-open-science-tools  here].
-−
-=== '''Assorted (offline and online) tools'''<br/> ===
-−
-*[https://www.docker.io Docker tool] - pack, ship and run applications as a lightweight container
-*[http://www.virtualbox.org VirtualBox] - create VM images
-*[http://www.occamportal.org OCCAM] - open curation for computer architecture modeling
-*[http://vida-nyu.github.io/reprozip ReproZip] - automatically packing experiments ([https://www.usenix.org/conference/tapp13/technical-sessions/presentation/chirigati related article])
-*[http://reproducible.io CARE tool] - Comprehensive Archiver for Reproducible Execution
-*[http://rr-project.org RR] - Mozilla project: records nondeterministic executions and debugs them deterministically
-*[http://www.pgbovine.net/cde.html CDE tool] - automatically create portable Linux applications with all dependencies
-*[http://ipython.org/notebook.html IPython Notebook] - a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document
-*[http://www.rstudio.com R-studio] - open source and enterprise-ready professional software for R
-*[https://www.codalab.org Codelab] - an experimental platform for collaboration and competition
-*[https://www.grid5000.fr Grid5000]  - large-scale and versatile testbed for experiment-driven research in all areas of computer science, with a focus on parallel and distributed computing including Cloud, HPC and Big Data
-*[http://www.mygrid.org.uk MyGrid] - develops a suite of tools designed to "help e-Scientists get on with science and get on with scientists"
-*[http://figshare.com FigShare] - managing research in a cloud
-*[http://www.runmycode.org RunMyCode] - online workflows
-*[https://www.aptlab.net AptLab] - online workflows
-*[http://www.taverna.org.uk Taverna] - designing and executing workflows
-*[http://boinc.berkeley.edu BOINC] - open-source software for volunteer computing and grid computing
-*[https://mulcyber.toulouse.inra.fr/projects/ngspipelines NGS pipelines] - integrates pipelines and user interfaces to help biologists to analyse data outputed from biological applications such as RNAseq, sRNAseq, ChipSeq, BS-seq
-*[http://www.seek4science.org SEEK for Science] - finding, sharing and exchanging Data, Models, Simulations and Processes in Science
-*[http://www.cs.umd.edu/projects/skoll/Skoll/Home.html Skoll] - a process & Infrastructure for Distributed, continuous Quality assurance
-*[http://nepi.inria.fr NEPI] - simplifying network experimentation
-*[http://pgbovine.net/burrito.html Burrito] - rethinking the Electronic Lab Notebook
-*[http://orgmode.org Org mode] - keeping notes, maintaining TODO lists, planning projects, and authoring documents with a fast and effective plain-text system
-*[http://hal.inria.fr/inria-00436029 open source cTuning technology] - towards collaborative and reproducible performance autotuning via public repository of optimization knowledge, crowdsourcing, machine learning and collective intelligence (2006-cur.)
-−
-=== '''Collective Knowledge Framework'''<br/> ===
-−
-*[http://github.com/ctuning/ck Collective Knowledge Framework] - tiny, open source, python application (~200Kb) to help researchers decompose their ad-hoc experimental workflows, benchmarks, data sets, scripts and VM/Docker images into reusable and customizable components with Python wrappers and unified JSON API while using already installed and possibly proprietary tools, benchmarks and data sets:
-−
-**[http://cknowledge.org/repo example of a CK-based interactive article with reproducible OpenCL autotuning experiments]
-**[http://github.com/ctuning/reproduce-clsmith PLDI'15 artifact converted to CK format]
-**[http://github.com/ctuning/reproduce-pamela-project Artifact repository for UK PAMELA project]
-**[http://github.com/ctuning/reproduce-carp-project Artifact repository for EU FP7 CARP project]
-**[http://github.com/ctuning/ctuning-programs Example of benchmarks shared in CK format]
-**[http://github.com/ctuning/ctuning-datasets-min Example of data sets shared in CK format]
-**[https://drive.google.com/folderview?id=0B-wXENVfIO82dzYwaUNIVElxaGc&usp=sharing Examples of CK repositories shared as zip files]
-**[http://github.com/ctuning/ck/wiki Full documentation]

@@ Line 30: / Line 30: @@
 === '''Collective Knowledge Framework'''<br/> ===
-*[http://github.com/ctuning/ck Collective Knowledge Technology] - preserve (with distributed ID), organize, desribe, share and reuse your code and data via GitHub
+*[http://github.com/ctuning/ck Collective Knowledge Framework] - tiny, open source, python application (~200Kb) to help researchers decompose their ad-hoc experimental workflows, benchmarks, data sets, scripts and VM/Docker images into reusable and customizable components with Python wrappers and unified JSON API while using already installed and possibly proprietary tools, benchmarks and data sets:
 **[http://cknowledge.org/repo CK-based interactive article]
 **[http://github.com/ctuning/reproduce-clsmith PLDI'15 artifact converted to CK format]
 **[http://github.com/ctuning/reproduce-pamela-project Artifact repository for UK PAMELA project]
@@ Line 38: / Line 39: @@
 **[http://github.com/ctuning/ctuning-datasets-min Example of data sets shared in CK format]
 **[https://drive.google.com/folderview?id=0B-wXENVfIO82dzYwaUNIVElxaGc&usp=sharing Examples of CK repositories shared as zip files]

@@ Line 27: / Line 27: @@
 *[http://orgmode.org Org mode] - keeping notes, maintaining TODO lists, planning projects, and authoring documents with a fast and effective plain-text system
 *[http://hal.inria.fr/inria-00436029 open source cTuning technology] - towards collaborative and reproducible performance autotuning via public repository of optimization knowledge, crowdsourcing, machine learning and collective intelligence (2006-cur.)
 *[http://github.com/ctuning/ck Collective Knowledge Technology] - preserve (with distributed ID), organize, desribe, share and reuse your code and data via GitHub
 **[http://cknowledge.org/repo CK-based interactive article]

@@ Line 3: / Line 3: @@
 === '''Assorted (offline and online) tools'''<br/> ===
-*[https://www.docker.io Docker tool] (pack, ship and run applications as a lightweight container)
+*[https://www.docker.io Docker tool] - pack, ship and run applications as a lightweight container
-*[http://www.virtualbox.org] (create VM images)
+*[http://www.virtualbox.org VirtualBox] - create VM images
 *[http://www.occamportal.org OCCAM] - open curation for computer architecture modeling
-*[http://vida-nyu.github.io/reprozip ReproZip] automatically packing experiments ([https://www.usenix.org/conference/tapp13/technical-sessions/presentation/chirigati related article])
+*[http://vida-nyu.github.io/reprozip ReproZip] - automatically packing experiments ([https://www.usenix.org/conference/tapp13/technical-sessions/presentation/chirigati related article])
-*[http://reproducible.io CARE tool from STMicroelectronics] (Comprehensive Archiver for Reproducible Execution)
+*[http://reproducible.io CARE tool] - Comprehensive Archiver for Reproducible Execution
-*[http://rr-project.org RR] (Mozilla project: records nondeterministic executions and debugs them deterministically)
+*[http://rr-project.org RR] - Mozilla project: records nondeterministic executions and debugs them deterministically
-*[http://www.pgbovine.net/cde.html CDE tool] (automatically create portable Linux applications with all dependencies)
+*[http://www.pgbovine.net/cde.html CDE tool] - automatically create portable Linux applications with all dependencies
-*[http://ipython.org/notebook.html IPython Notebook] (a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document)
+*[http://ipython.org/notebook.html IPython Notebook] - a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document
-*[http://www.rstudio.com R-studio] (Open source and enterprise-ready professional software for R)
+*[http://www.rstudio.com R-studio] - open source and enterprise-ready professional software for R
-*[https://www.codalab.org Codelab] (an experimental platform for collaboration and competition)
+*[https://www.codalab.org Codelab] - an experimental platform for collaboration and competition
-*[https://www.grid5000.fr Grid5000]  large-scale and versatile testbed for experiment-driven research in all areas of computer science, with a focus on parallel and distributed computing including Cloud, HPC and Big Data
+*[https://www.grid5000.fr Grid5000]  - large-scale and versatile testbed for experiment-driven research in all areas of computer science, with a focus on parallel and distributed computing including Cloud, HPC and Big Data
 *[http://www.mygrid.org.uk MyGrid] - develops a suite of tools designed to "help e-Scientists get on with science and get on with scientists"
-*[http://figshare.com FigShare] (managing research in a cloud)
+*[http://figshare.com FigShare] - managing research in a cloud
-*[http://www.runmycode.org RunMyCode] (online workflows)
+*[http://www.runmycode.org RunMyCode] - online workflows
-*[https://www.aptlab.net AptLab] (online workflows)
+*[https://www.aptlab.net AptLab] - online workflows
-*[http://www.taverna.org.uk Taverna] (designing and executing workflows)
+*[http://www.taverna.org.uk Taverna] - designing and executing workflows
-*[http://boinc.berkeley.edu BOINC] (open-source software for volunteer computing and grid computing)
+*[http://boinc.berkeley.edu BOINC] - open-source software for volunteer computing and grid computing
-*[https://mulcyber.toulouse.inra.fr/projects/ngspipelines NGS pipelines] (integrates pipelines and user interfaces to help biologists to analyse data outputed from biological applications such as RNAseq, sRNAseq, ChipSeq, BS-seq)
+*[https://mulcyber.toulouse.inra.fr/projects/ngspipelines NGS pipelines] - integrates pipelines and user interfaces to help biologists to analyse data outputed from biological applications such as RNAseq, sRNAseq, ChipSeq, BS-seq
 *[http://www.seek4science.org SEEK for Science] - finding, sharing and exchanging Data, Models, Simulations and Processes in Science
-*[http://www.cs.umd.edu/projects/skoll/Skoll/Home.html Skoll] (A process & Infrastructure for Distributed, continuous Quality assurance)
+*[http://www.cs.umd.edu/projects/skoll/Skoll/Home.html Skoll] - a process & Infrastructure for Distributed, continuous Quality assurance
-*[http://nepi.inria.fr NEPI] (Simplifying network experimentation)
+*[http://nepi.inria.fr NEPI] - simplifying network experimentation
-*[http://pgbovine.net/burrito.html Burrito] (Rethinking the Electronic Lab Notebook)<br/>[http://hal.inria.fr/inria-00436029 open source cTuning technology] (crowdsource auto-tuning and combine with machine learning using big data, predictive analytics and crowdsourcing) (2006-cur.)
+*[http://pgbovine.net/burrito.html Burrito] - rethinking the Electronic Lab Notebook
-*[http://c-mind.org/repo Collective Mind technology] (towards collaborative, systematic and reproducible computer engineering using big data, predictive analytics and collective intelligence) (2011-2014)
 *[http://orgmode.org Org mode] - keeping notes, maintaining TODO lists, planning projects, and authoring documents with a fast and effective plain-text system
 *[http://github.com/ctuning/ck Collective Knowledge Technology] - preserve (with distributed ID), organize, desribe, share and reuse your code and data via GitHub
 **[http://cknowledge.org/repo CK-based interactive article]

@@ Line 29: / Line 29: @@
 *[http://pgbovine.net/burrito.html Burrito] (Rethinking the Electronic Lab Notebook)<br/>[http://hal.inria.fr/inria-00436029 open source cTuning technology] (crowdsource auto-tuning and combine with machine learning using big data, predictive analytics and crowdsourcing) (2006-cur.)
 *[http://c-mind.org/repo Collective Mind technology] (towards collaborative, systematic and reproducible computer engineering using big data, predictive analytics and collective intelligence) (2011-2014)
-*[http://http://www.occamportal.org OCCAM project] - open curation for computer architecture modeling
+*[http://www.occamportal.org OCCAM project] - open curation for computer architecture modeling