Reproducible Research, LaTeX & Scientific Writing
This guide gathers tools, platforms, and methodologies for reproducible computational research, mathematical typesetting with LaTeX, and effective statistical communication.
1. Reproducible Research & Computational Workflows
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) ⚠️
Laboratory Information Management Systems
- LIMS.com: education on LIMS deployment ⚠️
- StarLIMS ⚠️
- Online Mouse Info System (mLIMS) ⚠️
- LabKey
- Mouse Colony
- UW-Madison Diabetes System
- RStudio
2. LaTeX & Mathematical Typesetting
LaTeX is a very powerful language for writing mathematical and statistical papers and books, developed by Don Knuth.
LaTeX Books
- Leslie Lamport (1986) LaTeX User’s Guide & Reference Manual, Addison-Wesley.
- Michael Goossens, Frank Mittelbach and Alexander Samarin (1993) The LaTeX Companion, Addison-Wesley.
LaTeX Links
- LaTeXit & KeyNote
- RStudio (has LaTeX tools now)
- TexMaker (cross platform tool)
- Graphics: Viewing & Printing
- Bold Font in Math Mode
- Landscape Orientation
- Using Auc-TeX under EMACS ⚠️
- LaTeX for Windows (emTeX)
- Yandell’s Notes on LaTeX
- Comprehensive TeX Archive Network (CTAN)
- Lyx document processor
- Google-docs and Latex ⚠️
- Latex Symbols
- Latex Symbols iPhone App ⚠️
- LaTeX Math WikiBooks
BibTeX Links
- Help On BibTeX (O’Reilly & Associates)
- Collection of Computer Science Bibliographies in BibTeX Format ⚠️
- Manipulating BibTeX Bibliographies ⚠️
- MA Inst Tech (MIT) IEEE BibTeX Database
3. Statistical Communication & Scientific Writing
Many of the links above have communication resources.
Communication Skills (giving professional talks)
- Brad Efron’s 13 Rules ⚠️
- Guidelines for Preparing Effective Presentations (Biometrics ENAR Section) ⚠️
- James Gee’s 14 Principles of Good Teaching & Good Learning
- Making Data Meaningful Guides(UN Econ Commission for Europe) ⚠️
- Presentation Tips (About.com) ⚠️
- Tips for Effective Presentation (Accu Conference) ⚠️
- Statistical Presentation Guidelines (Nat U Singapore)
- Presenting Statistics on Web Sites (John Maslin, Geowise)
- Guidelines for Statistical Analysis and Data Presentation (Ecological Society of America)
- Creativity and Learning: A Conversation with Lynda Barry (lynda.com)
- The Care and Feeding of the Biostatistician ⚠️ & the Scientist Collaborator ⚠️ (Elizabeth Matsui & Roger Peng)
- Biologist Talks to Statistician (video)
- Communicating Statistical Findings to Consulting Clients Operating in a Decisionmaking Climate: Best and Worst Practices (Ghement Stat Cons) ⚠️
- ASA Statistical Consulting Section ⚠️
Technical Writing
- LaTeX has for years been the standard for writing beautiful math expressions and with the advent of versions like pdflatex, xelatex and lualatex it is very convenient to produce PDF files. The big drawback to PDF is that the formatting is fixed in the file - you can’t “reflow” the text. HTML and epub formats allow reflowing of text so that you can easily read a document on a tablet or even a smartphone. However, you usually lose the beautiful math formatting.
- MathJax.org provides a way of incorporating high-quality math expressions in HTML for reading in a browser. The Rmd translator built into RStudio allows the use of MathJax markup, which is essentially the same as LaTeX expressions. MathJax is also available in IPython notebooks and IJulia notebooks. These are interactive web documents but can be converted to static HTML pages. Doug Bates created Mathjax static HTML for the MixedModels.jl Julia package ⚠️. Wes Brooks included MathJax typesetting in a blog written in Markdown and served via Django.
- Prefered slide package with Rstudio/RMarkdown: xaringan. Other options are Beamer with LaTeX and Reveal.js.