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 …
Note: Updated November 30, 2022 Chateaubriand Fellowship The Chateaubriand Fellowship allows PhD students registered in an American university the opportunity to spend 4–9 months in France. The fellowship aims to initiate or reinforce collaborations or join projects between French and American research teams. US citizenship is not required (see eligibility (slow archived link) and guidelines.) …
New classroom, computers, workshops New Apple Macintosh M1 computers are ready for hosting new workshops in person again. Apple M1 Macintosh The classroom is now equipped with Macintosh mac-mini computers with the new M1 chip. These are attached to Dell 4K display monitors providing a crisp image and easy connections. New workshops While there are many …
Cryo-Electron Microscopy Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures (i.e. very cold!.) For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. (See more on the Wikipedia article Cryogenic electron microscopy.) The following links are videos meant to present cryo-EM visually. Unfortunately, …
Becoming a Data Scientist If you are interested to become a data scientist, the following free resources and books would be very helpful. Free books using R These and other books aan be accessed for free on bookdown.org (Note: bookdown is the software used to edit them.) Free books on using Python Free books on …
UW personnel has access to Box, a cloud drive to store documents. While the older “Box Sync” application kept a copy of every file and folder on the local computer, the newer “box drive” software keeps only chosen folders or files on the local machine, everything else stays in the “cloud.” The location of …