Difference between revisions of "Reproducibility:Links"

Revision as of 11:54, 27 October 2015

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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 Framework

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:

@@ 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://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]
@@ 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]
+**[http://github.com/ctuning/ck/wiki Full documentation]