BOL: Related items

Computational Biology in the 21st Century: Making Sense out of Massive Data

Thu, 29 Aug 2013 08:32:26 -0500

Computational Biology in the 21st Century: Making Sense out of Massive Data Air date: Wednesday, February 01, 2012, 3:00:00 PM Category: Wednesday Afternoon Lectures Description: The last two decades have seen an exponential increase in genomic and biomedical data, which will soon outstrip advances in computing power to perform current methods of analysis. Extracting new science from these massive datasets will require not only faster computers; it will require smarter algorithms. We show how ideas from cutting-edge algorithms, including spectral graph theory and modern data structures, can be used to attack challenges in sequencing, medical genomics and biological networks. The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. Author: Dr. Bonnie Berger Runtime: 00:58:06 Permanent link: http://videocast.nih.gov/launch.asp?17563

Some useful Bioinformatics links

Jit — Fri, 16 Mar 2018 20:50:10 -0500

Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/18/2559/2475628
Reference-free SNP detection: dealing with the data deluge

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083407/
GATB/DiscoSnp: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

https://github.com/GATB/DiscoSnp
De novo assembly | Oxford Nanopore Technologies

https://nanoporetech.com/taxonomy/term/131
De novo long-read assembly of a complex animal genome | bioRxiv

https://www.biorxiv.org/content/early/2017/09/10/187054
Rapid de novo assembly of the European eel genome from nanopore sequencing reads | Scientific Reports

https://www.nature.com/articles/s41598-017-07650-6.epdf?author_access_token=dktG7e98wyRJnaEEMTcPqtRgN0jAjWel9jnR3ZoTv0P7E7t-wVGo30iojNO7dICajNY_7PE5xVPv6OoLe7hn9TeUjcZ5umREOzNoPMWkfYH58RS6uxm3vm4e4BG2AA_WKW84i6egKK271NwMq-NfzA%3D%3D
nanoporetech/ont-assembly-polish: ONT assembly and Illumina polishing pipeline

https://github.com/nanoporetech/ont-assembly-polish
Generade-nl/TULIP: TULIP - The Uncorrected Long read Itegration Pipeline

https://github.com/Generade-nl/TULIP
www.nature.com

https://www.nature.com/articles/s41598-017-03996-z
Example gallery of NanoPlot – Gigabase or gigabyte

https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/
Tool documentation

https://broadinstitute.github.io/picard/command-line-overview.html
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. - PubMed - NCBI

https://www.ncbi.nlm.nih.gov/pubmed/24185095
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
Measuring the distance between multiple sequence alignments | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/28/4/495/212883
The MUMmer 3 examples

http://mummer.sourceforge.net/examples/
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/tips.html
Omega | Overlap-graph de novo Assembler for Metagenomics

https://omega.omicsbio.org/
abiswas-odu/Disco: Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler

https://github.com/abiswas-odu/Disco
SAGE: String-overlap Assembly of GEnomes | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-302

Fast and sensitive mapping of nanopore sequencing reads with GraphMap | Nature Communications

https://www.nature.com/articles/ncomms11307
lumpy-sv/extractSplitReads_BwaMem at master · arq5x/lumpy-sv

https://github.com/arq5x/lumpy-sv/blob/master/scripts/extractSplitReads_BwaMem
jts/nanocorrect: Experimental pipeline for correcting nanopore reads

https://github.com/jts/nanocorrect

video - how to install flash plugin on ubuntu 14.04 LTS 64-bit version - Ask Ubuntu

https://askubuntu.com/questions/469553/how-to-install-flash-plugin-on-ubuntu-14-04-lts-64-bit-version
lh3/fermi: A WGS de novo assembler based on the FMD-index for large genomes

https://github.com/lh3/fermi
Multi-metagenome

http://madsalbertsen.github.io/multi-metagenome/docs/step9.html
Bandage by rrwick

https://rrwick.github.io/Bandage/
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/15/2210/2391162
Genome Architecture and Evolution of a Unichromosomal Asexual Nematode - ScienceDirect

https://www.sciencedirect.com/science/article/pii/S096098221731076X?via%3Dihub#fig4
How to determine chimeras in my de novo assembly? - SEQanswers

http://seqanswers.com/forums/showthread.php?t=26721
samtools(1) manual page

http://www.htslib.org/doc/samtools.html
How To Filter Mapped Reads With Samtools

https://www.biostars.org/p/56246/
The MUMmer 3 manual

http://mummer.sourceforge.net/manual/#nucmer
assembly_olc.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf
SAM and BAM filtering oneliners

https://gist.github.com/davfre/8596159
Inroduction to dot-plots

http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76
RepeatFinder Home Page

http://www.cbcb.umd.edu/software/RepeatFinder/
RepeatFinderReprint.pdf

http://www.cbcb.umd.edu/software/RepeatFinder/RepeatFinderReprint.pdf
https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html
Circular Visualization in R

http://zuguang.de/circlize_book/book/introduction.html#a-qiuck-glance
Creating a coverage plot using BEDTools and R

https://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
Eval: A software package for analysis of genome annotations | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-50
eval-documentation.pdf

http://mblab.wustl.edu/media/software/eval-documentation.pdf
OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921174/
sequence - download.tardigrades.org > v1 > sequence

http://download.tardigrades.org/v1/sequence/
ksahlin/BESST: BESST - scaffolder for genomic assemblies

https://github.com/ksahlin/BESST
reubwn/scripts: Useful scripts for various things

https://github.com/reubwn/scripts
ICEberg

http://db-mml.sjtu.edu.cn/ICEberg/index.php
Satsuma - Evolution and Genomics

http://evomics.org/learning/genomics/satsuma/
A complete bacterial genome assembled de novo using only nanopore sequencing data | Nature Methods

https://www.nature.com/articles/nmeth.3444
vezzi/FRC_align: Computes FRC from SAM/BAM file and not from afg files

https://mail.google.com/mail/u/0/#inbox
Read GTF file into R - Dave Tang's blog

https://davetang.org/muse/2017/08/04/read-gtf-file-r/

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html
Dot: Interactive dot plot for genome-genome alignments

https://dnanexus.github.io/dot/
Zoho Accounts

https://accounts.zoho.eu/signin?servicename=ZohoProjects&serviceurl=https%3A%2F%2Fprojects.zoho.eu%2Fportal%2Favaga2
lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://github.com/lh3/minimap2
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211
Palindromic gene amplification — an evolutionarily conserved role for DNA inverted repeats in the genome | Nature Reviews Cancer

https://www.nature.com/articles/nrc2591
bioinformatics - BLAST DNA Sequences Reversed - Biology Stack Exchange

https://biology.stackexchange.com/questions/8160/blast-dna-sequences-reversed
LASTZ

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
SOGo - (1652) Inbox

https://sogo.unamur.be/SOGo/so/jnarayan/Mail/view
Tetra-Nucleotide Analysis (TNA) | BIOiPLUG Help center

http://help.bioiplug.com/tetra-nucleotide-analysis-tna/

Clustering metagenomic contigs on tetranucleotide frequency — CGAT documentation

http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html

Interview Puzzles for Bioinformatician !

Rahul Nayak — Tue, 17 Jul 2018 05:26:18 -0500

These are some of the most famous Interview Puzzles being asked in top tech companies.

Here is a list of Top 25 puzzles which have been asked in top Tech Interview.

Specially for Microsoft Interview Puzzles, you may refer,
Top 15 Microsoft Interview Puzzles
Microsoft Interview Puzzles

Other MOST COMMON Interview Puzzles-
Top 25 Tech Interview Logical Puzzles

Each of the puzzles got repeated a number of times in interviews even for top tech companies

Rdatamining.com : R and Data Mining

Poonam Mahapatra — Thu, 15 Aug 2013 18:37:23 -0500

This website presents examples, documents and resources on data mining with R.
Documents on using R for data mining are available to download for non-commercial personal use, including R Reference card for Data Mining, R and Data Mining: Examples and Case Studies and Time Series Analysis and Mining with R.

Address of the bookmark: http://www.rdatamining.com/

Bioinformatics Programme Officer @ International Centre for Genetic ICGEB Engineering and Biotechnology

Fri, 23 Nov 2018 03:50:16 -0600

The following vacancies are available in the DBT Apex Biotechnology Information project at ICGEB, New Delhi, India. These positions are available for a period of approx. two years, however, initial appointment offer will be for 6 months, which will be extended based on performance of work. Salaries will be offered as per DBT, educational qualification and experience. Depending on requirements, selected candidates may be required to work on location from the Department of Biotechnology, New Delhi. Shortlisted candidates will be invited for an interview at ICGEB. Only the selected candidates will be informed individually. No TA/DA or accommodation will be offered to the candidates attending the interview.

4 Programme Officer 1
5 Technical Research Assistant 1

Minimum Educational Qualification, desirable experience and expected duties:

4: The applicants should be Postgraduates with experience in Data collection and Statistics, especially in Biotechnology-related data.

Expected duties: Collection of Biotechnology related information from India, to facilitate the Apex BTIC experts committee review of programmes at centres and R&D programs funded by DBT.

5: The applicants should be Postgraduates in Science with experience in Bioinformatics-related projects.
Expected duties: The candidates will assist the senior staff of the centre in daily activities and help in the preparation of the Annual Training Calendar, seminar and training podcasts/videos, repository of training material and Apex BTIC Newsletter.

Interested candidates should submit their full, updated Curriculum Vitae with a detailed description of relevant experience, along with two references by December 14th, 2018, addressed to, The Chairperson, DBT- Apex BTIC, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, Email: abtic@icgeb.res.in, kindly write “Application for DBT Apex BTIC vacancy” in the subject of the email or envelope, if sending by post.

Advertisement: http://www.icgeb.org/tl_files/Vacancies/dbt-abtic-vac-annmntrevsk.pdf

Most Commonly used Awk by Bioinformatician

Neel — Mon, 19 Aug 2013 01:12:38 -0500

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/

BINC Exam merged with DBT- BET JRF Exam

Jit — Thu, 21 Feb 2019 09:37:36 -0600

Another breaking news received has been received from the Department of biotechnology – DBT. As per a notification released by DBT, Bioinformatics National Certification (BINC) Exam conducted once per year by DBT has been now merged with DBT- BET JRF Exam.

Also, Bioinformatics Industrial Training Program (BIITP) is merged with the HRD Biotechnology Industrial Training Programme (BITP).

While this comes as a surprise for a lot of participants. We believe this is a good attempt to unify and create a national benchmark for talent. And we appreciate this endeavor from Department of biotechnology.

However, such last-minute announcements can create confusion. Thus candidates are advised to go through the complete notification DBT-BET JRF 2019 via the link below.If you have any kind of doubts, you must contact DBT JRF or Biotecnika for any kind of help & assistance.

Attention:-Bioinformatics Programs (BINC and BIITP)

1. Bioinformatics National Certification (BINC) has been merged with DBT-Junior
Research Fellow (BET Exam)

2. Bioinformatics Industrial Training Program (BIITP) is merged with HRDBiotechnology Industrial Training Programme (BITP).

Students of Bioinformatics, who are interested to apply for Fellowship or Industrial
Training may keep track of the advertisement of DBT-JRF (BET Exam) and BITP
of DBT.

More at http://www.bcil.nic.in/files/Attention_Bioinformatics_Programs_(BINC_and_BIITP).pdf

PhD at National Institute for Research in Reproductive Health

Fri, 30 Aug 2013 04:50:35 -0500

National Institute for Research in Reproductive Health

(Indian Council of Medical Research )
Jehangir Merwanji Street, Parel, Mumbai 400 012

Advertisement No. 1/NIRRH/Ph.D. 2013
Admission to Ph.D. Programme – 2013

National Institute for Research in Reproductive Health, Mumbai, a premier institute of the Indian Council of Medical Research, conducts basic, clinical and operational research in different areas of reproductive health. The thrust areas of research include: Fertility Regulation, Infertility and Reproductive Disorders, Reproductive Tract Infections, Maternal and Child Health, Osteoporosis, Genetic Disorders, Stem Cell Biology, Structural Biology, Bioinformatics and Reproductive Toxicology. Institute is affiliated to the University of Mumbai for the award of Ph.D. degree in Applied Biology, Biochemistry, Life Sciences and Biotechnology. The institute invites applications from young and bright students for enrollment in Ph.D. programme.

More at http://www.nirrh.res.in/announcements/phd_program_2013.htm

Bioinformatics web development course

Jit — Wed, 06 Nov 2019 20:42:48 -0600

This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics.

No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.

Address of the bookmark: http://www.cellbiol.com/bioinformatics_web_development/introduction/

Baumbach Lab

Wed, 21 Aug 2013 10:56:35 -0500

The Computational Biology research group was established in October 2012 at the Department of Mathematics and Computer Science (IMADA) at the University of Southern Denmark (SDU). It emerged from the Computational Systems Biology group, founded in March 2010 at the Max Planck Institute for Informatics (MPII) and the Cluster of Excellence for Multimodel Computing and Interaction (MMCI) at Saarland University, Saarbrücken, Germany.

The group is headed by Prof. Dr. Jan Baumbach and currently hosts nine PhD students and one postdoctoral fellow at both, IMADA/SDU and MMCI/MPII.

More at >> http://www.baumbachlab.net/