BOL: Related items

Coronavirus Resources !

Neel — Wed, 25 Mar 2020 17:11:33 -0500

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

Computational resources for TE discovery and TE detection

Abhimanyu Singh — Mon, 12 Feb 2018 10:29:18 -0600

Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis.

Following are the list of resource and location for TE discovery and TE detection:

BLASTER suite http://urgi.versailles.inra.fr/development/blaster/

Censor http://www.girinst.org/censor/download.php

find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl

FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm

HMMER http://hmmer.janelia.org/

LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/

LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7

LTR_par http://www.eecs.wsu.edu/~ananth/software.htm

MAK http://wesslercluster.plantbio.uga.edu/mak06.html

MaskerAid http://blast.wustl.edu/maskeraid/

mer-engine http://mer-engine.cshl.edu/mer-home.php

mreps http://bioinfo.lifl.fr/mreps/

PILER http://www.drive5.com/piler/

PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl

RepBase http://www.girinst.org/

RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/

RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm

RepeatMasker http://www.repeatmasker.org/

RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html

RepeatScout http://repeatscout.bioprojects.org/

repeat-match http://mummer.sourceforge.net/

REPuter http://www.genomes.de/

RetroMap http://www.burchsite.com/bioi/RetroMapHome.html

SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder

Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html

Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html

TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html

TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html

TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/

Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm

WU-BLAST http://blast.wustl.edu

Bioinformatics JRF/SRF position at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY

Sun, 11 May 2014 22:29:12 -0500

NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY
LBS, CENTRE, PUSA CAMPUS, IARI NEW DELHI
NEW DELHI – 110 012

WALK- IN –INTERVIEWS

Eligible candidates may appear in Walk-in-Interview on May 23, 2014 at 10 AM for the posts of Research Associates & Senior Research Fellows (SRF) in the following DST/DBT/ICAR funded projects.

1 NPTC Project on Bioinformatics and Comparative Genomics

Research Associate (One)

Rs. 24000/- + 30% HRA for masters degree holder with more than 4 years experience

Essential: Ph D in Plant Molecular Biology & Biotechnology/Genetics 0r Candidates who have already submitted their Ph D thesis in above subjects

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Senior Research Fellow ( UGCCSIR/ DBT/ ICAR Net qualified only): (One)

Rs. 16000/- + 30% HRA and Rs. 18000+30 HRA from 3rd year onwards

Essential:

1. ICAR/ UGCCSIR/DBT Net qualified only

2. M. Sc. (with thesis) in Biotechnology, Life Sciences, Biosciences/ Bioinformatics, Genetics/ Plant Pathology with experience in molecular biology.

Or M.Sc with more than 3 years research experiences

3. B.Sc. Agriculture or Biology

Desirable:
1. M. Sc. with thesis
2. Experience in molecular biology, plant tissue culture
3. Bioinformatics knowledge is important

2 DST JC Bose National Fellowship

Research Associate (Bioinformatics) : One

Rs.22000/- + 30% HRA for 1 & 2nd Yr., Rs. 23000+ 30% HRA for 3rd year and Rs. 24000+30% HRA for 4th &5th yr

Essential: M Ph D in Plant Molecular Biology & Biotechnology/Genetics

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Age limit: Max.35 years (Age relaxation of 5 years for SC/ST & women and 3 years for OBC)

The posts are purely temporary in nature and are co-terminus with the project. Initially the offer will be made for one year only and may be further extendable based on performance of the candidate. The interview will be held on May 23 , 2014 at 10:00 AM at NRCPB, LBS Building, Pusa Campus, IARI, New Delhi- 110012. The candidates must bring four copies of biodata (in the prescribed proforma), original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph. No. TA/DA would be given for the appearance in interview. Only the candidates having essential qualification would be entertained for the interviews. Short-listing of candidates based on academic merit and experience will be done in case of large number of applicants.

Advertisement: http://www.nrcpb.org/sites/default/files/Advertisement%20for%20RA%20and%20SRF%20Position.pdf

Free resources to learn statistics

BioStar — Sat, 06 Jul 2024 10:30:50 -0500

Welcome to the course notes for STAT 414: Introduction to Probability Theory. These notes are designed and developed by Penn State's Department of Statistics and offered as open educational resources. These notes are free to use under Creative Commons license CC BY-NC 4.0.

A free online version of the second edition of the book based on Stat 110, Introduction to Probability by Joe Blitzstein and Jessica Hwang, is now available at http://probabilitybook.net

Print copies are available via CRC Press, Amazon, and elsewhere.

Stat110x is also available as an edX course. Free signup at https://www.edx.org/course/introduction-to-probability-0

The edX course focuses on animations, interactive features, readings, and problem-solving, and is complementary to the Stat 110 lecture videos on YouTube, which are available at https://goo.gl/i7njSb

The Stat110x animations are available within the course and at https://goo.gl/g7pqTo

https://projects.iq.harvard.edu/stat110/home

Address of the bookmark: https://online.stat.psu.edu/stat414/

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

EMBO Practical Course, Bioinformatics, large-scale data, at Shenzhen, China

Wed, 14 Aug 2013 09:50:56 -0500

This international advanced course will provide training on bioinformatics and statistics methods for genomic research. It will give insight into how biological knowledge can be generated from high-throughput sequencing (DNA-Seq, RNA-seq, ChIP-seq) experiments and will illustrate how to analyze such data. The course covers both the underlying statistical and algorithmic concepts, and the practice of how to automate and code such analyses using the scripting language R.

17 Nov 2013 -22 Nov 2013

More at http://events.embo.org/13-large-scale-data/

Online Registration: https://www.conference-service.com/pc13-47/welcome.cgi

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

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/

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.