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=== '''Assorted (offline and online) tools'''<br/> === | === '''Assorted (offline and online) tools'''<br/> === | ||
| − | *[https://www.docker.io Docker tool] | + | *[https://www.docker.io Docker tool] - pack, ship and run applications as a lightweight container |
| − | *[http://www.virtualbox.org] | + | *[http://www.virtualbox.org VirtualBox] - create VM images |
*[http://www.occamportal.org OCCAM] - open curation for computer architecture modeling | *[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 | + | *[http://reproducible.io CARE tool] - Comprehensive Archiver for Reproducible Execution |
| − | *[http://rr-project.org RR] | + | *[http://rr-project.org RR] - Mozilla project: records nondeterministic executions and debugs them deterministically |
| − | *[http://www.pgbovine.net/cde.html CDE tool] | + | *[http://www.pgbovine.net/cde.html CDE tool] - automatically create portable Linux applications with all dependencies |
| − | *[http://ipython.org/notebook.html IPython Notebook] | + | *[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] | + | *[http://www.rstudio.com R-studio] - open source and enterprise-ready professional software for R |
| − | *[https://www.codalab.org Codelab] | + | *[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://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] | + | *[http://figshare.com FigShare] - managing research in a cloud |
| − | *[http://www.runmycode.org RunMyCode] | + | *[http://www.runmycode.org RunMyCode] - online workflows |
| − | *[https://www.aptlab.net AptLab] | + | *[https://www.aptlab.net AptLab] - online workflows |
| − | *[http://www.taverna.org.uk Taverna] | + | *[http://www.taverna.org.uk Taverna] - designing and executing workflows |
| − | *[http://boinc.berkeley.edu BOINC] | + | *[http://boinc.berkeley.edu BOINC] - open-source software for volunteer computing and grid computing |
| − | *[https://mulcyber.toulouse.inra.fr/projects/ngspipelines NGS pipelines] | + | *[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.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] | + | *[http://www.cs.umd.edu/projects/skoll/Skoll/Home.html Skoll] - a process & Infrastructure for Distributed, continuous Quality assurance |
| − | *[http://nepi.inria.fr NEPI] | + | *[http://nepi.inria.fr NEPI] - simplifying network experimentation |
| − | *[http://pgbovine.net/burrito.html Burrito] | + | *[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://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://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] | **[http://cknowledge.org/repo CK-based interactive article] | ||
Revision as of 09:33, 26 October 2015
Assorted (offline and online) tools
- Docker tool - pack, ship and run applications as a lightweight container
- VirtualBox - create VM images
- OCCAM - open curation for computer architecture modeling
- ReproZip - automatically packing experiments (related article)
- CARE tool - Comprehensive Archiver for Reproducible Execution
- RR - Mozilla project: records nondeterministic executions and debugs them deterministically
- CDE tool - automatically create portable Linux applications with all dependencies
- IPython Notebook - a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document
- R-studio - open source and enterprise-ready professional software for R
- Codelab - an experimental platform for collaboration and competition
- 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
- MyGrid - develops a suite of tools designed to "help e-Scientists get on with science and get on with scientists"
- FigShare - managing research in a cloud
- RunMyCode - online workflows
- AptLab - online workflows
- Taverna - designing and executing workflows
- BOINC - open-source software for volunteer computing and grid computing
- NGS pipelines - integrates pipelines and user interfaces to help biologists to analyse data outputed from biological applications such as RNAseq, sRNAseq, ChipSeq, BS-seq
- SEEK for Science - finding, sharing and exchanging Data, Models, Simulations and Processes in Science
- Skoll - a process & Infrastructure for Distributed, continuous Quality assurance
- NEPI - simplifying network experimentation
- Burrito - rethinking the Electronic Lab Notebook
- Org mode - keeping notes, maintaining TODO lists, planning projects, and authoring documents with a fast and effective plain-text system
- 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 Technology - preserve (with distributed ID), organize, desribe, share and reuse your code and data via GitHub
