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, …
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 …
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 below shows only the R and Python courses. See complete listing at https://sscc.wisc.edu/sscc_jsp/training/ Title Date Time Instructor Introduction to Python …
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 the main author and curator of the web site which was started to disseminate virus depictions based on X-ray crystallography …
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 Caprentries at UW Madison as reported by this carpentry blog by UW–Madison Lauren Michael, now Lead Research Computational Facilitator at …
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 get some idea of what the subject is about. For example I wrote a series of 4 posts titled Do …
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 require a high memory (RAM) footprint, and/or extremely large data files. Biochemistry Department personnel can obtain access to the in-door …
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. This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use the …
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.
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).