Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – Biochem – Social Science Computing Cooperative (SSCC) – UW Libraries – SSteenbock Library Workshops – Computational Biology, Ecology, …
python
Python NumPy 2.0 incompatibilities
Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested …
Rosetta Ligand Docking – Help with Docker
Summary Combine software and scripts on Docker and local macOS computer (Intel amd64 or arm64 Silicon Chip M series) to follow successfully the Rosetta tutorial Ligand Docking with a G-Protein Coupled Receptor. This method will …
POSE: build, manipulate, mutate, L, D, protein molecular structures
Summary Pose is a Python library for building and manipulating protein molecular structures. Builds with L- and D- amino acids or a mixture; can open existing PDB structures. Computes many molecular properties. Pose Library Pose …
R and Python workshops on Campus – Winter 2024
Summary Workshop Series available on Campus on R and Python: – Biochem – Social Science Computing Cooperative (SSCC) – UW Libraries – SSteenbock Library Workshops – Computational Biology, Ecology, & Evolution (ComBEE) Study Groups …
Faster image creation in PyMOL: Shortcuts and Docker
Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while …
AlphaFold2 with full databases and multimer option
Summary This article describes running AlphaFold2 with full databases at the UW-Madison Center for High Throughput Computing (CHTC) and is part of an article series titled Five ways to run AlphaFold. CHTC cluster, HTCondor, Containerization …
Centralizing R & Python Data Projects: Posit Cloud Essentials Event
Cloud event Users of RStudio may be interested in this monthly event presented by “Posit” which is the new name of the company that produces RStudio, as the software can be used with many more …
R and Python workshops on Campus – Fall 2023
Summary Workshop Series available on Campus on R and Python: Biochem SSCC UW Libraries R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed but …
AlphaFold2 on Macintosh M1
Summary This post is a summary of installation of AlphaFold2 onto a Macintosh with an M1 style (arm64) computer chip (i.e. not an Intel/AMD Chip.) This post started with the blog post Installing Alphafold2 on …