BOL: Related items

Understanding pango networks !

Abhi — Sat, 16 Oct 2021 14:02:36 -0500

In the vast majority of instances it is expected that Pango lineage names and designations will conform to the following rules. These rules also act as guidelines for the decisions made by the Lineage Designation Committee.

https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/

https://www.pango.network/how-does-the-system-work/what-are-pango-lineages/

Reference paper

https://www.nature.com/articles/s41564-020-0770-5

Address of the bookmark: https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/

Bioinformatics Training Material !

BioStar — Sat, 18 Mar 2023 11:26:18 -0500

Glittr is a curated list of bioinformatics training material.
All material is:

In a GitHub or GitLab repository
Free to use
Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

J-Circos

Shruti Paniwala — Fri, 17 Feb 2017 09:06:54 -0600

Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

Pimp your brain: Bioinformatics

Wed, 20 Aug 2014 22:09:21 -0500

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de

NGS teaching material

Jit — Wed, 05 Apr 2017 04:29:06 -0500

High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html

Hello Python World !

Rahul Nayak — Mon, 14 May 2018 16:41:01 -0500

As I mentioned earlier, I will keep on posting one Python script per day to introduce you to Python programming. Whether you are an experienced programmer or not, this tutorial is intended for everyone who wishes to learn the Python programming language.

Python is a very simple language, and has a very straightforward syntax. The simplest directive in Python is the "print" directive - it simply prints out a line (and also includes a newline).

Create a file Hello.py

print("Hello, Python World !.")

Run

python3 Hello.py

Bioinformatics in Africa: Part 4 - Morocco

BioStar — Sat, 06 Feb 2021 13:31:24 -0600

Bioinformatics, in the UFR in Artificial Intelligence and Bioinformatics, deals with the management, the analysis, the modelling and the visualization of biological databases. Since the size of the databases is often exponential, the traditional algorithms are not very effective when seeking for a good computational solution.

To take care of this issue, many ways are opened to the researchers to improve the quality of the algorithms:

1. Usage of new information processing methods like artificial neuronal networks, genetic algorithms, etc. 2. Usage of Data mining to explore biochemical databases,
3. Usage of Machine learning on the biological examples to solve, for example, the problem of classification in Bioinformatics.

UFR offers in addition a doctoral training in Computer Science and Bioinformatics.

Doctoral module which includes: a Diplôme des Etudes Supérieures Approfondies (DESA) of two years; and a doctorate studies program with a national Ph.D. certification. Three specializations constitute the teaching trunk of the ENSAT: Computer engineering, Telecom engineering, and electronic systems engineering.

Research Interest and Activities:

The following are the present areas of research interest:

1. Machine Learning and Profile Gene Expression of Cancer
2. Predicting Protein structure
3. Hidden Markov Models (HMMs) and multiple alignments
4. Transformational Grammar for sequence modelling
5. Physical Mapping: STSs
6. Evolutionary Computation applied to Genomic and Proteomic
7. Predicate Logic and Protein Structure

Web site and links:

http://www.ensat.ac.ma/udiab http://www.pasteur.fr/pasteur/international/annonce_coursBioinfoannonce06_casa.pdf

List of useful machine / ai learning resources !

Rahul Nayak — Tue, 30 Mar 2021 08:56:06 -0500

ML cheatsheet !

https://github.com/remicnrd/ml_cheatsheet

Visual AI / ML

https://setosa.io/ev/

Simple and efficient tools for predictive data analysis

https://scikit-learn.org/stable/

Apache server setting !

Abhi — Fri, 29 Oct 2021 04:29:51 -0500

Apache is an open source web server that’s available for Linux servers free of charge.

In this tutorial we’ll be going through the steps of setting up an Apache server.

What you’ll learn

How to set up Apache
Some basic Apache configuration

Address of the bookmark: https://ubuntu.com/tutorials/install-and-configure-apache#3-creating-your-own-website

Programming for Lovers !

BioStar — Tue, 07 Nov 2023 23:56:30 -0600

Programming for Lovers (P4❤️) is a free online course that teaches programming using the Go programming language by immersing learners in fun scientific applications.

Each chapter focuses on a single scientific problem and contains a core text accompanied by code alongs and autograded exercises.

You can meet Phillip Compeau in our intro video. Phillip has taught programming at Carnegie Mellon University for years and is a serial online education founder. He is thrilled to bring you this course.

Address of the bookmark: https://programmingforlovers.com/