6 Sites For Free Alternative Textbooks
(Excerpt from: Info from UW News – Posted by Erik Geiger on August 27, 2018)
[…] Engineers, and other STEM majors will want to check out MIT Open Courseware.
Open Culture
Free textbooks (aka open textbooks) written by knowledgable scholars are a relatively new phenomenon. Open Culture offers 200 Free Textbooks.
MIT Open Courseware
MIT OpenCourseWare is a web-based publication of virtually all MIT course content. OCW is open and available to the world and is a permanent MIT activity.
Textbook Revolution
Textbook Revolution is a student-run site dedicated to increasing the use of free educational materials by teachers and professors.
Wikibooks
Wikibooks is an open-content textbooks collection that anyone can edit.
Project Gutenberg
Project Gutenberg offers over 56,000 free, public domain eBooks in multiple formats. Topics include English and international literature, foreign languages, history, mathematics, and language instruction.
OpenStax
OpenStax offers peer reviewed, open source textbooks are written by professional content developers who are experts in their fields.
Software
UW-system software library
Molecular graphics
AutoDock
AutoDock Vina
MODELLER
UCSF Chimera
UCSF ChimeraX
PyMOL, (for UW distribution)
Sybyl (See instructors)
Data Analysis
Commercial packages
MATLAB (for UW distribution)
Python
python.org
Anaconda.com
Jupyter.org
R/RStudio
Genomics
Databases
Protein Data Bank (PDB – 3D)
Worldwide PDB (wwPDB)
America’s PDB – Research Collaboratory for Structural Bioinformatics
Protein Data Bank in Europe
Protein Data Bank Japan
BMRB – Biological Magnetic Resonance Data Bank
PDB 101 / Molecule of the month
VIPERdb – Virus Particle Explorer.Scripps
3-Dimensional Electron Microscopy
Unified Data Resource for 3DEM
Electron Microscopy Data Bank (EMDB) at PDBe (Europe)
3D electron microscopy data navigator (Japan)
VIPER EMBD (Virus Particle Explorer. Scripps)
Genomics
GEO – Gene Expression Omnibus
ArrayExpress – functional genomics data
Sequence Read Archive (SRA)
Protein, DNA, RNA, genome sequence databases
Nucleotides
GenBank (NCBI – NIH)
RefSeq: NCBI Reference Sequence
European Nucleotide Archive
Protein
PIR – Protein Information Resource
UniProt (sequence and functional information)
External tutorials
Molecular Graphics
Autodock / Autodock Vina Tutorials (HTML)
MODELLER Tutorials (HTML)
Practical Pymol for Beginners (HTML – 2018)
Introduction to PyMOL (PDF – 2009)
Sybyl Tutorials (HTML – 2002)
UCSF Chimera Tutorials (HTML)
UCSF ChimeraX Tutorials (HTML)
R / RSTudio tutorials
R for Beginners (E. Paradis – PDF)
R Tutorial (cyclist.org)
Learn R Programming (tutorialspoint.com)
Learn R Programming | R examples (datamentor.io)
R Course: R Tutorial for Beginners: Learning R Programming (guru99.com)
R Markdown
RStudio Learning: R programming, Markdown etc. (RStudio.com)
R Markdown: The Definitive Guide (HTML ebook)
blogdown: Creating Websites with R Markdown (HTML ebook) – (PDF version)
Python
Educba Python Tutorial (from Basics and detailed “blog style” entries.
Machine Learning in Python (scikit-learn.org) | Examples
External tutorials: Software Carpentry
Complete list of software carpentry lessons
R/RStudio
Programming with R
R for Reproducible Scientific Analysis
Data Analysis and Visualization in R for Ecologists
SQL databases and R
Español: R para Análisis Científicos Reproducibles
Python
Programming with Python
Plotting and Programming in Python
Python Testing and Continuous Integration
MATLAB
Databases and SQL
Cheat-Sheets
Cheat sheets can be useful as a memory back-up. When I learned Latin, it was stressed that before looking into the lexicon, one should first try to retrieve the information from memory first. It may be there. Then, if needed, look into cheat sheet, which can sometimes be a challenge too given the information concentration. Cheat sheets come in various formats, which can sometimes be called quick reference guide instead.
Molecular graphics
- PyMOL: PymolRef.pdf, PyMOL Cheat Sheet Source Code (zip)
- Chimera: quickref.pdf
- ChimeraX: User guide (HTML)
- VMD: vmd_cheatsheet.pdf, vmd-tutorial.pdf
RStudio / R
RStudio provides a large series of cheat sheets that encompass a wide range of subjects. The page is located at rstudio.com/resources/cheatsheets and covers R, python, R markdown and many specific R packages.
Programming
- Python 3: python-cheat-sheet
- SQL: sql-cheat-sheet
- MySQL: mysql-cheat-sheet
(Note: These are from web site websitesetup.org that offers further cheatsheets that are more relevant to web development such as JavaScript, PHP or HTML.)