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 …
Computing
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).
AlphaFold background
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
VMWare and EFI partition
I have been a Macintosh user since 1986 but it is still necessary once in a while to access a Windows system and that is why VMWare Fusion is installed on my iMac which has …
Do yourself a favor: learn Markdown – Episode 4. Reproducible reports
The message The essential message is this: stop using Copy/Paste from one program to another (e.g. a chart from Excel to Word) as this is a manual process that is not reproducible and can easily …
Google colab is a free cloud notebook environment
Introduction Google Colab is a free cloud-based service that allows the execution of Python code using the Jupyter Notebook format. It is possible to use and install new python libraries. Furthermore it is possible to …
Download Google Drive Files using wget
The problem: transfer file between clouds Files on Google drive can be shared between users, but the default access to the file is via a web browser graphical interface. However, sometimes it may be useful, or even …
Data Analysis Workshops Winter 2021
SUMMARY: Check calendar for Free “R” and “Python” workshops (Steenbock Library.) “Introduction to R with RStudio,” “Data Wrangling in R” (SSCC – Social Science Computing Cooperative.) “Automating Tasks with the Unix Shell,” “Data Management with SQL,” “R: introduction / visualization / reports” (Software Carpentry through UW-Madison Data Science (fees apply).)