Enabling open science tools

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Assorted (offline and online) tools

• Collective knowledge framework developed by the community - small, portable and customizable framework to share artifacts as reusable Python components with JSON API; quickly prototype experimental workflows (such as multi-objective autotuning); automate, crowdsource and reproduce experiments; unify predictive analytics (scikit-learn, R, DNN); enable interactive articles.
  • Many CK summer news including several open projects with ARM and General Motors on artifact sharing and reproducible experimentation
  • open optimization repository to collaboratively crowd-tune shared workloads among platforms provided by volunteers
  • Android app connected to CK to crowdsource experiments via mobile phones and tablets
  • Caffe converted to CK to crowd-benchmark and crowdtune this DNN framework
  • PLDI'15 artifact converted to CK (OpenCL crowd-testing)
  • PACT'16 artifact converted to CK (multi-objective SLAM autotuning)
  • Artifact repository for EU FP7 CARP project (polyhedral optimization)
  • Example of benchmarks shared in CK format
  • Example of data sets shared in CK format
  • Examples of CK repositories shared as zip files
  • Full documentation

• DataMill: a community-based, easy-to-use, open source infrastructure for performance evaluation
• Software Heritage - preserving software
• PRISMA: transparent reporting of systematic reviews and meta-analyses
• Consort: transparent reporting of trials
• Umbrella and Parrot for reproducible research;
• Mozilla Science Lab -- Code as a Research Object
• "Minimal metadata schemas for science software and code, in JSON and XML"
• Open Science Framework
• EUDAT: the collaborative Pan-European infrastructure
• ScienceExchange: main website; reproducibility page
• Travis CI: Test and Deploy with Confidence
• Sumatra: automated tracking of scientific computations
• R+OpenScience: Transforming science through open data
• 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 - enabling collaborative and reproducible performance autotuning via public repository of optimization knowledge, crowdsourcing, machine learning and collective intelligence (2006-cur.)

If you would like to discuss our open science initiative, do not hesitate to get in touch via CK mailing list!