Inspired by article “How to set up and run Python Data Science Development Environment with Jupyter on Docker” [Archived] Data Scientists that write or use code must work with a variety of Data Science development tools, including the Anaconda (or Miniconda) Python distribution platform, the Python programming language, the R programming language, Matplotlib library, Pandas Library, the Jupyter application, and many others. Installing …
What is PATH There are many technical definitions that can be found, but in simple terms, PATH is a list of directories.The listed directories will contain the software that run on the computer, including the command-line programs. PATH is a variable, and thus this list is flexible and new directories can be added. When the …
Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement of previous version – Adding an alternate Python: Anaconda – Could Docker help? Python mess? The problem with Python is …
Summary This book will be used to learn Python in workshop settings. For Biologists, Life Scientists There are many books, even free books, with the objective to teach Python or other programming languages. I previously wrote a list of free books on the post Free Data Science Books. This book “Python for the Life Sciences …
Summary New generations lack the concepts of files and folders organization as they rely on search methods or search engines to find what they need. In 2017, astronomer Catherine Garland first noticed the issue. Her students were modeling turbines for jet engines using simulation software as she taught an engineering course. Students kept calling her …
Free courses This new page lists professional courses available to UW–Madison personnel at LinkedIn Learning (previously Lynda.com) and just requires a NetID. The page has been added on the new “Software Resources” top menu for an easy find, and is also listed below: The page is: Free programming courses The page also lists courses that …
Summary A web site to create BibTex entries for bibliography in R Markdown. R and Markdown This is a follow-up on 4 “Episodes” in previous posts titled “Do yourself a favor: learn Markdown…” To add bibliographical information it is necessary to write the information of a paper in the BibTex format. BibTeX-files may contain four …
Summary The PyMOD 3 version of the plug-in provides GUI interface within PyMOL for many bioinformatics tools such as BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE, and MODELLER. Web page: http://schubert.bio.uniroma1.it/pymod/ GitHub: https://github.com/pymodproject/pymod Reference Giacomo Janson, Alessandro Paiardini, PyMod 3: a complete suite for structural bioinformatics in PyMOL, Bioinformatics, Volume 37, Issue 10, 15 May 2021, …
NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resources PyMOL resources Summary This post provides resources on PyMOL What is PyMOL and how to get it The University of Wisconsin participates in the licensing of PyMOL Campus wide. License and software are available on the Campus …
NCBI BLAST Workshop The NCBI workshop is designed for beginning BLAST users or people wanting a refresher on how blast works and some tips on how to run effective BLAST searches. – Materials: 2022-10_Basic-Web-BLAST – Slides, PDF: workshop_BLAST_Oct2022.pdf – Recording: has been added (See Workshop Video Tab on Materials page.) This workshop is suitable both …