Category: Computing

Webinar Data visualisation principles for enhancing effective scientific communication

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“Data visualisation principles for enhancing effective scientific communication” Webinar Announcement: “Live Training” This webinar will provide an introduction to data visualisation principles. It includes a review of basic concepts and showcases tools to improve your understanding and use of data visualisation for improved accessibility to your research. Link: https://www.ebi.ac.uk/training/events/data-visualisation-principles-enhancing-effective-scientific-communication/ Quick Info:  Register Date: 26 June …

PyMOL and Biological Units from REMARK 350

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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 …

New Tutorial Section: Computational Modeling

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Computational Modeling This is the general title of a new Tutorials pull-down menu that will be populated with new or updated tutorials. It can be found within the Tutorials menu list as Computational Modeling The very first tutorial is the result of an update to a Rosetta tutorial for “ligand docking” and adapt the Linux-based …

Rosetta Ligand Docking – Help with Docker

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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 …

POSE: build, manipulate, mutate, L, D, protein molecular structures

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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 …

AlphaFold A practical guide Online Tutorial – EBI-EMBL

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Summary This Free EBI/EMBL on-line course “AlphaFold, A practical guide” provides an understanding of the fundamental concepts behind AlphaFold2, how users can run protein predictions and integrate these predictions into their projects, and how AlphaFold2 has been used to enhance research. Course info Cost: Free Time to complete: 3 hours Resources required: Google Account (computation …

NCBI-Workshops

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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 …

R and Python workshops on Campus – Winter 2024

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  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 R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed …

Is p-value hacking reverse statistics?

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Summary P-value hacking is the process of manipulating or analyzing data in a way that increases the likelihood of obtaining statistically significant results. I used 4 different AI chatbots to obtain an explanation with examples. Statistics This story came about when I watched a short video titled “Teach me STATISTICS in half an hour! Seriously.” …

Do yourself a favor: learn Markdown – Episode 7: BibTeX for online articles

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Summary A tool to create a BibTeX entry for online articles or blogs. Generate BibTeX from URL This is a follow-up on 6 “Episode”” in previous posts titled “Do yourself a favor: learn Markdown…” In a previous article (Sgro (2022)) I presented how to add bibliographical information within an Rmarkdown document (Allaire et al. (2023)) …