Reproducible Research Tools
Reproducible Research Tools This is an eclectic collection of links about reproducible research. Some of these will be relevant to Online & Blended Courses, probably for advanced topics, and some are more relevant to research.
- Workflow Systems
- Publishing & Communications
- Genomics Platforms
- Small Molecule Interaction Databases
- Laboratory Information Management Systems
- Scaling up / High Throughput & High Performance Computing
- Reproducible Research Forum
- Software Carpentry R for Reproducible Scientific Research
Workflow Systems
- Transparency in Computational Science (talk by Victoria Stodden)
- Dissemination Platforms: IPOL | Madagascar | MLOSS.org | nanoHUB.org | vHUB.org | Open Science Framework | runmycode.org | thedatahub.org
- Wiley’s WIREs Computational Molecular Science
- Laboratory for Optical and Computational Instrumentation (LOCI) | Open Microscopy (OME) | Fedora Commons
- Triple Store
- EnterpriseWeb | MioSoft
Publishing & Communications
- Open access publishing: A researcher’s perspective (Karl Broman, Oct 2013)
- Literate computing” and computational reproducibility: IPython in the age of data-driven journalism (Fernando Perez)
- Workflow Tracking and Research Environments: CDE | Kepler | Paper Mache (PDF) | Pegasus | Sumatra | Taverna | VisTrails
- Embedded Publishing: Verifiable Computational Research | Collage Authoring Environment | SHARE knitr & Sweave
- Hypothesis.is: Collaborative Evaluation of Information
- Speak Up, the Internet Can’t Hear You (NY Times, Apr 2013)
Open Access and Other Journals
- Scholarly Publishing and Academic Resources Coalition (SPARC)
- Open Access Scholarly Publishers Association (OASPA)
- Directory of Open Acces Journals (DOAJ)
- Highly Regarded Open Access Journals: Project Euclid & PLoS
- Statistical Science Web Journals List
- Web of Knowledge Master Journal List
- NIH PubMed Journals List
- JSTOR Journals
- Beall’s List of Predatory Publishers (See Cautionary Tales below)
Cautionary Tales
- Who’s Afraid of Peer Review? (Science, Oct 2013) (see SPARC, OASPA & DOAJ Responses)
- Bad Science (Language Log, Oct 2013)
- The open access hoax and other failures of peer review (Language Log, Oct 2013)
- Scientific Articles Accepted (Personal Checks, Too) (NY Times, Apr 2013)
- Sponsors Now Pay for Online Articles, Not Just Ads (NY Times, Apr 2013)
- The Past, Present and Future of Scholarly Publishing (Michael Eisen, Mar 2013)
- Scholarly Open Access: Critical Analysis of Publishing (J Beall, U CO Denver)
Genomics Platforms
- The anatomy of successful computational biology software (Nature, Nov 2013)
- Sage Bionetworks Repository: Synapse
- GenomeSpace | GenePattern | Galaxy
- eQTL Viewer
- Mouse Genome Informatics: Phenotypes, Alleles & Disease Models
- PhenoGen Informatics (CO U)
- eXtensible Genotype And Phenotype platform (XGAP)
- MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen
- Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA
- .NET bio (Microsoft Bioinformatics Platform)
- iPlant | caBIG
- Institute for Systems Biology
- Scaling in Random Networks, Barabasi
- R & Bioconductor
Small Molecule Interaction Databases
- BioMart | R/biomaRt
- BioGRID: Biological General Repository for Interaction Datasets
- Molecular Libraries Program
- KEGG: Kyoto Encyclopedia of Genes and Genomes
- Gene Ontology (GO) | R/gostats
- NIH Mouse Knockout Project: IKMC | KOMP
- Rat Genome Database: Knockout Rat Consortium
- AgriKOLA: Arabidopsis Genomic RNAi Knock-out Line Analysis
- Institute of Bioinformatics and Systems Biology/MIPS: Mammalian PPI Database | Yeast PPI (CYGD)
- Finley Lab Links to PPI Databases
- PPI Databases, Data Collections, & Webtools
- Center for Cancer Systems Biology Links, Harvard U
- Transfac: Gene Regulation
- JASPAR Database
- Arabidopsis Database (AtTFDB)