Data analysis tools and resources
- Deeper look at git rebase
- EdX courses on data analysis for genomics
- Joel Spolsky explaining how to use Excel and notes.
- Slidedeck from Jenny Bryan keynote on spreadsheets
- Review hosted on github discussing large genome assembly with PacBio Long Reads
- Sinaplots – alternative to violin plots and boxplots
- Video showing support vector machine separating classes – https://www.youtube.com/watch?v=3liCbRZPrZA
- How random forest decision trees work from Shape of Data blog
Writing and scientific publishing
- YouTube playlist featuring videos from Stanford statistician and writing consultant Kristen Sainani
- Kristen Sainani’s self-paced, on-line science writing course (adapted from her Coursera class) https://med.stanford.edu/cme/courses/online/writing15.html
- How to write a scientific abstract in six easy steps by Steve Easterbrook, University of Toronto.
- Advice for writing a review from an editor of a scientific journal
- Atlantic Monthly article on The Needless Complexity of Academic Writing
- Dr. Karen’s foolproof grant-writing template
- Articles and ‘How to’ guides for science writing from the Wellcome Trust: http://blog.wellcome.ac.uk/tag/swp2014/
- The Science Writers’ Handbook – http://pitchpublishprosper.com/
Computer science education
- Obtaining a thorough background in computer science on-line – with links to courses
Bioinformatics and genomics
- The DIY scientist, the Olympian, and the mutated gene – How a woman whose muscles disappeared discovered she shared a disease with a muscle-bound Olympic medalist
- Susan Lindquist discusses protein folding and disease.
- Jennifer Doudna explains CRISPR/Cas genome editing
- NCBI developers page with links to NCBI git repo, web services documentation, and more.
- Twitter bot that reports papers covering alternative splicing and cancer
- User-friendly software for designing constructs for genome engineering, expression constructs, and more – SnapGene
- On-line whiteboard: https://awwapp.com. Useful for collaborations.
- We use Basecamp project management software. We like it a lot.
- We also use Jira issue tracking software with agile plugin from Atlassian. We like it a lot, too.
- Google flights, useful for finding out where you can go, direct, for cheap
- Advice on how to print a fabric poster (for scientific meetings) by Jessica Polka
Women in statistics, bioinformatics, and computer science
- Miriah Meyer, from the School of Computing, University of Utah, studies and develops data visualization systems.
- Nomi Harris is Project Manager for the KBase project. She also co-organizes the annual Bioinformatics Open Source Conference (BOSC).
- Doreen Ware leads a plant-focused bioinformatics research team at Cold Spring Harbor Laboratory. Her group develops and supports Gramene.
- Alicia Oshlack develops statistical methods for analysis of biological data, such as the GOSeq R package.
- Alison Motzinger-Reif teaches statistical consulting and analyzes clinical trials data at NC State.
Sites with images from Integrated Genome Browser
- Laboratory Web site of Crisanto Gutiérrez at Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid.
- Research page from the Dorsett Lab Web site, at St. Louis University.
- Periodic table of bioinformatics tools
- The Science Web, Onion for bioinformatics
- The Silicon Valley tarot card deck. Ann’s favorite: the stockholder.
- The big red button that doesn’t do anything.
- Jamie Zawinski’s the Netscape dorm. Everything changes, everything stays the same.