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. …
Computing
Accessing BOX on macOS with command line
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” …
R and Python workshops – Fall 2022
Summary Check the Calendar listing for data analysis workshops links and registration forms. Below are workshop dates for SSCC, Madison chapter of Software Carpentry, and Steenbock Library series. Social Science Computing Cooperative (SSCC) The table …
Where is VirusWorld?
Virusworld. was hosted since its inception at the Institute for Molecular Virology in 1993/1994 at the dawn of the World Wide Web and was retired on the first week of July 2022. I was …
Software Carpentry
The Carpentries The University of Wisconsin-Madison is a Platinum Member Organization of the THE CARPENTRIES that comprise 3 communities: the Software Carpentry, Data Carpentry, and Library Carpentry. There is a lot of enthusiasm around the …
Learn X in Y minutes
Learn X in Y minutes In the past we had “flash cards” to memorize and review materials. This site Learn X in Y minutes has one-page reminders that can be used to re-learn material or …
Guide to Submitting HTCondor jobs
High Throughput Computing (HTC) First a note: HTC is meant for a large number of small to medium size jobs. HTC is different than HPC (High Performance Computing) that would run large size jobs that …
AlphaFold – How to interpret structures
3D Protein structure prediction (4) This YouTube video from the European Bioinformatics Institute – EMBL-EBI webinar was recorded on 08 September 2021 This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. …
AlphaFold – run from ChimeraX
The new ChimeraX menu “Tools > Structure Prediction > AlphaFold” provides a simple interface to run AlphaFold2 Colab that does not require the user to know how to use a Jupyter Notebook.
AlphaFold code
DeepMind and Google have created a method to access the code on GitHub. All the details to install AlphaFold locally are on the “readme” page, visible on the lower portion of the GitHub page ColabFold (See my Blog: Google colab is a free cloud notebook environment).