BOL: Related items

Advanced Bash-Scripting Guide

Jit — Thu, 18 Feb 2016 04:50:51 -0600

This tutorial assumes no previous knowledge of scripting or programming, yet progresses rapidly toward an intermediate/advanced level of instruction . . . all the while sneaking in little nuggets of UNIX® wisdom and lore. It serves as a textbook, a manual for self-study, and as a reference and source of knowledge on shell scripting techniques. The exercises and heavily-commented examples invite active reader participation, under the premise that the only way to really learn scripting is to write scripts.

This book is suitable for classroom use as a general introduction to programming concepts.

More at http://tldp.org/LDP/abs/html/

Address of the bookmark: http://tldp.org/LDP/abs/html/

BBTools User Guide

Neel — Mon, 11 Dec 2017 06:37:48 -0600

The guides describe the function, syntax, and typical use-cases of the tools; for a complete list of parameters, run the tool’s shellscript or open it with a text editor. Most tools do not currently have a guide, but each has shellscripts with basic usage information. The “General Usage Guide” gives shared background information covering usage of all tools.

Installation

General Usage Guide

Data Preprocessing Guide

Specific Tool Guides:

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

Address of the bookmark: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

Machine Learning !!!

Gudiya Pal — Fri, 01 Jul 2016 12:57:12 -0500

In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

An Introduction to Applied Bioinformatics

Jit — Fri, 02 Mar 2018 04:26:38 -0600

IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and information on my research and lab on my lab website.

Address of the bookmark: http://readiab.org/

Bioinformatics in Africa: Part3 - Mali

BioStar — Sat, 06 Feb 2021 13:28:44 -0600

International Center for Excellence in Research (ICER):

The ICER is a research center composed of the following three programs: 1. The Malaria Research and Training Center Parasitology Group, 2. The Malaria Research and Training Center Entomology Group 3. The SEREFO Group.

The first two programs develop biomedical researches in malaria, Filariasis and Leishmaniasis. The third program develops biomedical researches in tuberculosis and HIV.

Bioinformatics was introduced recently to the ICER and is constantly growing. The ICER has one team, headed by Sidy SOUMARE, which supports the three programmes in all their needs in informatics and bioinformatics. This team can beneficiate from some computational facilities (4 blast servers, 15 other servers and around 200 terminals), but the ICER staff needs some training in order to be able to administrate these facilities.

Research Interest and Activities: The following are the present areas of research interest: 1. Functional genomics 2. Analysis of microarray data 3. Interaction between the vector and the parasite.

Bioinformatics in Africa: Part7 - Tunisia

BioStar — Sat, 06 Feb 2021 21:25:09 -0600

Institut Pasteur de Tunis (IPT):
The IPT is a research institution founded in 1883. IPT is under the supervision of the Ministry of Health and is part of the Université El Manar of Tunis (Ministry of high Education). The missions of the institute are: Public Health Laboratory activities (PHL), Research on infectious diseases, and R/D on vaccines. Research programs are mainly oriented towards local health problems such as leishmaniais, viral hepatitis, and scorpion venoms. The group of Bioinformatics and Modelling of the IPT is hosted by the Laboratoire d’Immunopathologie Vaccinologie et Génétique Moléculaire (LIVGM), and exists since the beginning of 2005. Its present research activities include: genome annotation, EST clustering and modelling of the host/parasite response to Leishmania infection. It consists of two senior scientists, two PhD students and one MSc student

Centre de Biotechnology de Sfax (CBS):
Bioinformatics activity started at CBS in 2001 with the settingup of a research and service unit of bioinformatics. This unit currently includes one senior researcher, one engineer and four Phd students. Activities include sequence annotation (service) and three research programs: ab initio prediction of short eukaryote genes, statistical modelling by Bayesian networks approach of signal transduction pathways and statistical analysis of human sequence variation data (haplotype reconstruction and linkage disequilibrium). Activities of the Bioinformatics unit could be found at the website: http://www.cbs.rnrt.tn/ and the research activity report is available under request to Bioinformatics@cbs.rnrt.tn. Although the computing facilities are good, there is still a need for trained human resources to strengthen bioinformatics capacities at CBS, particularly in structural bioinformatics.

Web site and links: http://www.cbs.rnrt.tn

Basic Structure of Snakemake Pipeline Run !

Abhi — Thu, 14 Oct 2021 07:01:38 -0500

/user/snakemake-demo$ ls

config.json data envs scripts slurm-240702.out Snakefile

data = mock data for the snakefile to use
Snakefile = name of the snakemake “formula” file
- Note: The default file that snakemake looks for in the current working directory is the Snakefile. If you would like to override that you can specify it following the -s
  - snakemake -s snakefile.py
envs = directory for storing the conda environments that the workflow will use.
scripts = directory for storing python scripts called by the snakemake formula.
config.json = json format file with extra parameters for our snakemake file to use.
cluster.json = json format file with specification for running on the HPC
samples.txt = file we will use later relating to the config.json file.

Run the snakemake file as a dry run (the example workflow shown above).

This will build a DAG of the jobs to be run without actually executing them.
snakemake --dry-run

User can execute rules of interest.

snakemake --dry-run all VS. snakemake --dry-run call VS. snakemake --dry-run bwa

Run the snakemake file in order to produce an image of the DAG of jobs to be run.

snakemake --dag | dot -Tsvg > dag.svg OR snakemake --dag | dot -Tsvg > dag.svg

Run the snakemake (this time not as a dry run)

snakemake --use-conda

Seeing Theory and Learn

LEGE — Tue, 04 Jun 2024 00:31:54 -0500

Seeing Theory was created by Daniel Kunin while an undergraduate at Brown University. The goal of this website is to make statistics more accessible through interactive visualizations (designed using Mike Bostock’s JavaScript library D3.js).

Address of the bookmark: https://seeing-theory.brown.edu/

DIY Transcriptomics

Abhi — Wed, 31 Jul 2024 01:19:26 -0500

A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real ‘omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.

https://diytranscriptomics.com

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

Interactive Bioinformatics Resources !

Jit — Thu, 12 Aug 2021 00:09:00 -0500

Learn how to use bioinformatics tools right from your browser.
Everything runs in a sandbox, so you can experiment all you want.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio