Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – UW Libraries – Steenbock Library Workshops – UW Data Science Hub / Software Carpentry – Social Science Computing Cooperative (SSCC) Steenbock Library Workshops See details on announcement page: Learn how to use Python and/or R programming languages for …
Summary ChatMol is a ChatGPT plugin that offers a Free chatlite version that does not require an API key. ChatMol ChatMol is a PyMOL plugin based on large language models, that provide a conversational interface (CUI) for molecular operation and computation. Current supported models include models from OpenAI (ChatGPT versions), Anthropic (Claude versions), DeepSeek, and …
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, & Evolution (ComBEE) Study Groups R and Python at Biochem R and Python “Clubs” were established in late 2022. The …
Summary We run a script to compute the distance between 2 atoms in a series of PDB files with identical molecules in different conformations and save the distance results into a plain text file. No GUI PyMOL In previous posts I explained how we can use PyMOL as a command-line tool from a Terminal when …
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 to implement a process involving Python packages from a paper published in 2019: “AlleleAnalyzer: a tool for personalized and allele-specific …
R and Tidyverse Tabular Data Analysis I have updated the Tabular data analysis with R and Tidyverse course that analyze environmental health data from National Health and Nutrition Examination Survey (NHANES) a survey research program conducted by the National Center for Health Statistics (NCHS) to assess the health and nutritional status of adults and children …
Summary Compute biological assembly from coordinates with a python script. Symmetry X-ray crystallography solved the mathematical problem to provide 3D (cartesian) coordinates but the resulting “asymmetric unit cell” does not necessarily represent the biological structure. The Protein Data Bank (PDB) now provides options to download the biological entity, which can contain a lesser number than …
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 allow to access the native OS speed while fulfilling all preparatory and exploratory steps that fail or are too complex …
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 is a Python library for building and manipulating protein molecular structures. From an amino acid sequence the user can create …
Summary The National Center for Biotechnology Information (NCBI) offers events, including workshops hands-on, interactive training sessions. All events are listed on the NCBI Outreach Events page. Workshop recordings and materials remain available after the live sessions. NCBI Outreach Events The National Center for Biotechnology Information (NCBI) is a division of the National Library of Medicine …