<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/23892?offset=700 https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu Fri, 31 Jan 2020 01:31:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu <![CDATA[Google Colab : Google Colab is a free cloud service and now it supports free GPU!]]> You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV. 

If you have just a single notebook to submit, use the website https://google-colab.com/, it is really easy, on the top right corner click 'submit +'. The earlier you post the more visibility you will get over time

Address of the bookmark: http://colab.research.google.com

]]> Jit https://bioinformaticsonline.com/researchlabs/view/10739/science-for-life-laboratory-scilifelab-sweden Sat, 10 May 2014 06:22:30 -0500 <![CDATA[Science for Life Laboratory (SciLifeLab)-Sweden]]> Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.

Webpage : https://www.scilifelab.se/about-us/
Opportunity: https://www.scilifelab.se/about-us/career/

]]> https://bioinformaticsonline.com/videolist/watch/4094/manufacturing-life-with-j-craig-venter Thu, 29 Aug 2013 08:52:26 -0500 https://bioinformaticsonline.com/videolist/watch/4094/manufacturing-life-with-j-craig-venter <![CDATA[Manufacturing Life with J. Craig Venter]]> J. Craig Venter, CEO of Synthetic Genomics, talks about finding genomic-driven solutions to address global needs such as new sources of energy, food and vaccines in an interview with James Bennet, Editor-in-Chief of The Atlantic. This program is introduced by Pradeep Khosla, the new chancellor of the University of California, San Diego. Series: "The Atlantic Meets The Pacific" [11/2012] [Public Affairs] [Show ID: 24359] The Atlantic Meets the Pacific playlist: http://goo.gl/5V8Yb The Atlantic Meets the Pacific on UCTV: http://www.uctv.tv/atlanticpacific UCTV: http://www.uctv.tv]]> https://bioinformaticsonline.com/news/view/19272/translate2r Fri, 21 Nov 2014 01:16:06 -0600 https://bioinformaticsonline.com/news/view/19272/translate2r <![CDATA[translate2R]]> After their presentation at the international “user!” conference, data analysis specialist eoda starts the public alpha testing of translate2R. With the start of alpha testing the innovative migration solution by the company hailing from Kassel discards the working title “translateR” and takes on the final product brand name “translate2R”. translate2R is a service for the automated translation of SPSS® syntax to R code, therefore supporting data analysts with a quick and low-risk migration to R.

The manual translation of many, frequently rather complex SPSS scripts often presents itself as a tedious and error-prone task, and represents a rather large obstacle for many analysts and companies to migrate to a modern, open source data management and analysis tool like R. With translate2R this hurdle will be diminished substantially.

Find at https://service.eoda.de/translater/?lang=en

]]> Rahul Nayak https://bioinformaticsonline.com/news/view/36191/bioinformatics-workshops-no-coding-required Mon, 09 Apr 2018 13:06:01 -0500 https://bioinformaticsonline.com/news/view/36191/bioinformatics-workshops-no-coding-required <![CDATA[Bioinformatics Workshops - NO CODING REQUIRED]]> Bioinformatics Workshops T-BioInfo

Pine Biotech, Inc., a US-based startup working with the Tauber Bioinformatics Research Center is offering a full curriculum online preparing students without any technical background for real-life challenges with large scale biomedical data. Workshops on processing, analysis and biomedical interpretation of Next Generation Sequencing data cover important up-to-date algorithms and machine learning approaches. The most important thing is that there are virtually no pre-requisites such as coding, biostatistics or advanced medical skills. If you know what gene is and how the genes are expressed, you are ready to take the courses or join our workshops. Learn more: https://edu.t-bio.info/workshops/

]]> eliabrodsky https://bioinformaticsonline.com/researchlabs/view/11107/the-minerva-research-group-for-bioinformatics Tue, 27 May 2014 15:48:14 -0500 <![CDATA[The Minerva Research Group for Bioinformatics]]> The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

]]> https://bioinformaticsonline.com/pages/view/37592/benchmarking-perl-module Sat, 25 Aug 2018 11:40:42 -0500 https://bioinformaticsonline.com/pages/view/37592/benchmarking-perl-module <![CDATA[Benchmarking Perl Module !]]> The benchmark module is a great tool to know the time the code takes to run. The output is usually in terms of CPU time. This module provides us with a way to optimize our code. With the advent of petascale computing and other multicore processor it is becoming a neccesity to know about the CPU time taken by our perl program.

This is the simple way to use the module

Example1:

use Benchmark;

$first_time = Benchmark->new;

our code……

$second_time = Benchmark->new;

$final_difference = timediff($first_time,$second_time);

print “the code took, timestr($final_difference),”\n”;

that was a very simple way to know the time diff , we can use it to know the time taken by some part of the code in the program.

More sophisticated way:

use Benchmark;
sub first {

my(arguments) = @_;

}

timethese(100, { first => ‘first_sub(arguments)’});

The first argument to timethese is 100 (evaluate 100 times).

Hope this very small tutorial with Benchmark will help people get started.

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/42003/perl-one-liner-for-beginners Fri, 24 Jul 2020 05:58:28 -0500 https://bioinformaticsonline.com/blog/view/42003/perl-one-liner-for-beginners <![CDATA[Perl one-liner for beginners !]]> I often use the following arguments to perl:

  • -e Makes the line of code be executed instead of a script
  • -n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin)
  • -p Forces your line to be called in a loop. Prints $_ at the end

 

  • This counts the number of quotation marks in each line and prints it
    perl -ne '$cnt = tr/"//;print "$cnt\n"' inputFileName.txt
  • Adds string to each line, followed by tab
    perl -pe 's/(.*)/string\t$1/' inFile > outFile
  • Append a new line to each line
    perl -pe 's//\n/' all.sent.classOnly > all.sent.classOnly.sep
  • Replace all occurrences of pattern1 (e.g. [0-9]) with pattern2
    perl -p -i.bak -w -e 's/pattern1/pattern2/g' inputFile
  • Go through file and only print words that do not have any uppercase letters.
    perl -ne 'print unless m/[A-Z]/' allWords.txt > allWordsOnlyLowercase.txt
  • Go through file, split line at each space and print words one per line.
    perl -ne 'print join("\n", split(/ /,$_));print("\n")' someText.txt > wordsPerLine.txt
  • or in other words, delete every character that is not a letter, white space or line end (replace with nothing)
    perl -pne 's/[^a-zA-Z\s]*//g' text_withSpecial.txt > text_lettersOnly.txt
  • perl -pne 'tr/[A-Z]/[a-z]/' textWithUpperCase.txt > textwithoutuppercase.txt;
  • Print only the second column of the data when using tabular as a separator
    perl -ne '@F = split("\t", $_); print "$F[1]";' columnFileWithTabs.txt > justSecondColumn.txt
  • One-Liner: Sort lines by their length
    perl -e 'print sort {length $a <=> length $b} <>' textFile
  • One-Liner: Print second column, unless it contains a number
    perl">perl -lane 'print $F[1] unless $F[1] =~ m/[0-9]/' wordCounts.txt
]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38378/gwaspro-a-high-performance-genome-wide-association-analysis-server Fri, 07 Dec 2018 08:04:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38378/gwaspro-a-high-performance-genome-wide-association-analysis-server <![CDATA[GWASpro: A High-Performance Genome-Wide Association Analysis Server]]> GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10,000 samples from replicable lines or hybrids. GWASpro provides an interface that significantly reduces the learning curve for new GWAS investigators.

 

Address of the bookmark: https://bioinfo.noble.org/GWASPRO/

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala