PyMOL Stereo viewing PyMOL can display stereo in many ways. Unless special equipment is available, the method is to split the PyMOL 3D view area in two with the command stereo on (and stereo offto turn it off.) The alternative is to use the menu cascade: Display > Stereo. However, there are 2 ways …
Registering for The New York Times through UW–Madison All necessary information can be found at: https://www.library.wisc.edu/help/research-tips-tricks/registering-for-the-new-york-times-through-uw-madison/ duplicated below: UW–Madison students, faculty, and staff have free access to The New York Times Digital (NYTImes.com) through the UW–Madison Libraries. Register for access and create an account by following the steps below. Registering for The New York Times Digital: …
Sequence Composition: fast shell method Motivation This post was inspired to “verify” a Python Script meant to compute the sequence composition of amino acids, as suggested by ChatGPT. (See ChatGPT_Protein_Composition.ipynb, or viewer ChatGPT_Protein_Composition.ipynb.) The code below is inspired by post number-of-occurences-of-letters-in-a-word. I found the process useful, and in addition applicable to nucleic acids as well. …
Python and Object-oriented programming Object-oriented programming (OOP) is a programming paradigm based on the concept of “objects“, which can contain data and code. The data is in the form of fields (often known as attributes or properties), and the code is in the form of procedures (often known as methods).(Wikipedia) Summary of OOP concepts I …
Intermediate Research Software Development in Python Greetings everyone and Club members, (apologies i you receive duplicates) This may be more of interest to intermediate/advanced Python users: A Spring Break mini course offered by the local chapter of Software Carpentry at the UW–Madison Data Science Hub, March 13th – 17th , 9am-1pm: This course aims …
Summary Pandoc is a document converter for multiple type of files. Converting example Format conversion is a chore that often takes a lot of time. I recently wanted to convert a long MSWord document into a version of Markdown that I could use to update a software documentation. Pandoc can convert many documents types into …
NCBI Magic-BLAST Workshop The intermediate level workshop Analyzing & Visualizing NextGen Reads with Magic-BLAST – [Archived] is designed for biologists who are comfortable working with the command-line (bash) and who are interested in performing some early analysis on their next-generation sequence data in comparison to an annotated reference sequence. – Materials: Analyzing & Visualizing NextGen Reads …
Summary Clarifying Python code containing the mysterious “dot notation” of object-oriented languages. An object is a combination of data stored within a specific class. A class is a blue-print (or framework) that defines attributes (containing the data) and methods that act as functions onto the data contained within the object. The “dot notation” makes the …
Summary Finding and implementing settings in RStudio to use Pyhon. RStudio and Python RStudio can handle a large number of languages (> 50) in addition to its basic support of R. (This month the RStudio company has been renamed Posit.) There are a few critical steps to implement for using Python to avoid painful issues, …
Summary Python ranks #1 in popularity of programming languages on the TIOBE Index TIOBE Index The popularity of programming languages is reflected in the TIOBE Programming Community index which is updated once a month. The rankings are determined by the amount of qualified engineers in the world, courses, and outside vendors using data from well-known …