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 …
Inspired by article “How to set up and run Python Data Science Development Environment with Jupyter on Docker” [Archived] Data Scientists that write or use code must work with a variety of Data Science development tools, including the Anaconda (or Miniconda) Python distribution platform, the Python programming language, the R programming language, Matplotlib library, Pandas Library, the Jupyter application, and many others. Installing …
What is PATH There are many technical definitions that can be found, but in simple terms, PATH is a list of directories.The listed directories will contain the software that run on the computer, including the command-line programs. PATH is a variable, and thus this list is flexible and new directories can be added. When the …
Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement of previous version – Adding an alternate Python: Anaconda – Could Docker help? Python mess? The problem with Python is …
Summary This book will be used to learn Python in workshop settings. For Biologists, Life Scientists There are many books, even free books, with the objective to teach Python or other programming languages. I previously wrote a list of free books on the post Free Data Science Books. This book “Python for the Life Sciences …
Summary New generations lack the concepts of files and folders organization as they rely on search methods or search engines to find what they need. In 2017, astronomer Catherine Garland first noticed the issue. Her students were modeling turbines for jet engines using simulation software as she taught an engineering course. Students kept calling her …