<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35534?offset=10 https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata Tue, 11 Jun 2019 21:27:10 -0500 https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata <![CDATA[Amity University Bioinformatics Summer Program - Kolkata]]> Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

]]> eliabrodsky https://bioinformaticsonline.com/bookmarks/view/43243/interactive-bioinformatics-resources Thu, 12 Aug 2021 00:09:00 -0500 https://bioinformaticsonline.com/bookmarks/view/43243/interactive-bioinformatics-resources <![CDATA[Interactive Bioinformatics Resources !]]> 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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material Sat, 18 Mar 2023 11:26:18 -0500 https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material <![CDATA[Bioinformatics Training Material !]]> 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

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/26539/scikit-learn Mon, 29 Feb 2016 17:39:24 -0600 https://bioinformaticsonline.com/bookmarks/view/26539/scikit-learn <![CDATA[scikit-learn]]> Machine Learning in Python

Simple and efficient tools for data mining and data analysis
Accessible to everybody, and reusable in various contexts
Built on NumPy, SciPy, and matplotlib
Open source, commercially usable - BSD license

More at http://scikit-learn.org/stable/index.html

 

Address of the bookmark: http://scikit-learn.org/stable/auto_examples/index.html

]]> Jitendra Prajapati https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician Mon, 19 Aug 2013 01:12:38 -0500 https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician <![CDATA[Most Commonly used Awk by Bioinformatician]]>  

Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.

Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.

choose rows where column 3 is larger than column 5:

awk '$3>$5' input.txt > output.txt

extract column 2,4,5:

awk '{print $2,$4,$5}' input.txt > output.txt

awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt

show rows between 20th and 80th:

awk 'NR>=20&&NR<=80' input.txt > output.txt

calculate the average of column 2:

awk '{x+=$2}END{print x/NR}' input.txt

regex (egrep):

awk '/^test[0-9]+/' input.txt

calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:

awk '{print $0,$2+$3}' input.txt

awk '{$1=$2+$3;print}' input.txt

join two files on column 1:

awk 'BEGIN{while((getline<"file1.txt")>0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt > output.txt

count number of occurrence of column 2 (uniq -c):

awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt

apply "uniq" on column 2, only printing the first occurrence (uniq):

awk '!($2 in l){print;l[$2]=1}' input.txt

count different words (wc):

awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt

deal with simple CSV:

awk -F, '{print $1,$2}'

substitution (sed is simpler in this case):

awk '{sub(/test/, "no", $0);print}' input.txt

 

OK now here's where to read this stuff properly explained. roll

Two thorough tutorials:

http://www.gnu.org/software/gawk/manual/gawk.html

http://www.grymoire.com/Unix/Awk.html

A famous list of useful one-liners - though they're short, many are quite tricky:

http://www.pement.org/awk/awk1line.txt

And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!

http://www.catonmat.net/blog/awk-one-li … -part-one/

http://www.catonmat.net/blog/ten-awk-ti … -pitfalls/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/42672/introduction-to-bioinformatics-and-computational-biology Mon, 25 Jan 2021 01:32:30 -0600 https://bioinformaticsonline.com/bookmarks/view/42672/introduction-to-bioinformatics-and-computational-biology <![CDATA[Introduction to Bioinformatics and Computational Biology]]> This is the course material for STAT115/215 BIO/BST282 at Harvard University.

Xiaole Shirley Liu (lead instructor)
Joshua Starmer
Martin Hemberg
Ting Wang
Feng Yue

Ming Tang
Yang Liu
Jack Kang
Scarlett Ge
Jiazhen Rong
Phillip Nicol
Maartin De Vries

We thank many colleagues in the community, who helped Dr. Liu in prepare the STAT115/215 BIO/BST282 course over the years. 

Address of the bookmark: https://liulab-dfci.github.io/bioinfo-combio/

]]> Jit https://bioinformaticsonline.com/pages/view/42815/bioinformatics-in-africa-part7-tunisia Sat, 06 Feb 2021 21:25:09 -0600 https://bioinformaticsonline.com/pages/view/42815/bioinformatics-in-africa-part7-tunisia <![CDATA[Bioinformatics in Africa: Part7 - Tunisia]]> 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

]]> BioStar https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory Wed, 18 Aug 2021 00:19:48 -0500 <![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory]]> Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR). CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

]]> https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42552/bioinformatics-workbook Tue, 05 Jan 2021 22:42:32 -0600 https://bioinformaticsonline.com/bookmarks/view/42552/bioinformatics-workbook <![CDATA[bioinformatics workbook]]> This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is referred to for more information throughout the book.

https://bioinformaticsworkbook.org/

Address of the bookmark: https://bioinformaticsworkbook.org/

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