Summary A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large sample files. Docker on Biochemistry Compute Cluster The HTCondor scheduler software on the Biochemistry Compute Cluster (BCC) can run Docker …
What is AlphaFold How to access AlphaFold There are multiple options to access AlphaFold. Here are four options using the limited databases. One options for the full databases. Using limited Databases: 1.) Casual users can use “Google Colab” with a web browser. Familiarity with Jupyter Notebook for running Python is helpful. The service is free …
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 languages beyond R, including Python. This event will occur monthly online on the last Tuesday of every month. Next occurrence …
Summary Workshop Series available on Campus on R and Python: R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed but may be restarted in a new format. Minutes and scripts from the sessions are available online: beginners, intermediate_advanced, communication. The R-Club is continuously meeting …
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 Apple Silicon. The installation will require about 8Gb of space. Installing AlphaFold2 AlphaFold2 is a trained Machine Learning set of …
What is Augmented Reality? Augmented Reality (AR) is an exciting technology that overlays virtual elements on top of the real world, allowing for a unique and immersive user experience. The Apple AR platform only uses the web browser “Safari” and does not require any plug-in or specialized software, only that portable electronics (iPhone, iPad) have …
Jupytext can save and reformat Jupyter notebooks I was trying to test a Jupyter notebook from NCBI titled “Getting Started with NCBI Data in Python” (March 2, 2022) that is now on a “Binder” web page. However, the system kept stalling, but I was given access to the “raw” script. To my surprise the format …
PyCharm IDE Installation Having “Admin privileges” on an educational or business computer is becoming a rarity, as security reasons are increasingly important. However, there are often way to install a software for “just one user” that can be useful. PyCharm is a popular Python Integrated development environment (IDE), a software application that helps manage writing computer code …
Intelligent Systems for Molecular Biology – in Madison The International Society for Computational Biology (ISMB) Conference held the Intelligent Systems for Molecular Biology (ISMB) in Madison in July 2022. Conference details are still available online, but more importantly a special “Bioinformatics” journal issue has been compiled from the proceedings of this conference: Most articles link to …
NCBI tutorial: iCn3D hands-on workshop “I see in 3D” (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode […] – (Longer description.) This workshop is designed for life scientists with some (intermediate) expertise in structural biology. The topics of structure prediction, molecular …