<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44640?offset=60 https://bioinformaticsonline.com/opportunity/view/39826/data-scientist-mwd Wed, 07 Aug 2019 03:19:46 -0500 <![CDATA[Data Scientist (m/w/d)]]> https://uk-erlangen.concludis.de/prj/shw/b8b26f24186191c7af8a25e2cc6115ca_0/27008/Data_Scientist_m_w_d.htm?b=0

Deadline: 30.09.2019

Requirement:
Microsoft SQL Server: Administration, Transact-SQL
Machine Learning
Know Deutsch und Englisch langauge

]]> https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases Wed, 12 Feb 2020 01:16:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases <![CDATA[Biological databases !]]> Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43013/deg-50-a-database-of-essential-genes-in-both-prokaryotes-and-eukaryotes Tue, 30 Mar 2021 11:47:29 -0500 https://bioinformaticsonline.com/bookmarks/view/43013/deg-50-a-database-of-essential-genes-in-both-prokaryotes-and-eukaryotes <![CDATA[DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes]]> Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43894/chembl Wed, 22 Jun 2022 23:09:26 -0500 https://bioinformaticsonline.com/bookmarks/view/43894/chembl <![CDATA[ChEMBL]]> ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

Address of the bookmark: https://www.ebi.ac.uk/chembl/

]]> Shruti Paniwala https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals Tue, 25 Apr 2017 05:03:27 -0500 https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals <![CDATA[List of GOI approved peer reviewed bioinformatics and computational biology journals]]> Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news – something many call “predatory publishing".  Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).

Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for “scientific journal” publication with little or no peer review. For a fee, they will publish almost anything – even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent “advocacy research.” You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/

Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.

Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:

NOTE:Each journal details are in following order Tittle\nSource\nSubject.
Point to remember: The list of journals are NOT sorted in any ascending or descending order.

If I missed any other GOI validated bioinformatics journal, then please report me in comment section.

Open Bioinformatics Journal
Scopus
Computer Science; Engineering; Medicine

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
WoS
BIOLOGY & BIOCHEMISTRY

Advances and Applications in Bioinformatics and Chemistry
Scopus
Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science

Advances in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering

Applied Bioinformatics
Scopus
Agricultural and Biological Sciences; Computer Science

BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Bioinformatics and Biology Insights
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics

BMC BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

BRIEFINGS IN BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Scopus
Medicine

Current Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Current Protocols in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology

JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS
ICI
BIOLOGICAL SCIENCE

Journal of integrative bioinformatics
Scopus
Medicine

Journal of Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Mathematical Biology and Bioinformatics
Scopus
Engineering; Mathematics

Trends in Bioinfprmatics
Scopus
Computer Science

Eurasip Journal on Bioinformatics and Systems Biology
Scopus
General; Computer Science; Mathematics; Medicine

Evolutionary Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Genomics, Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE-ACM Transactions on Computational Biology and Bioinformatics
WoS
COMPUTER SCIENCE

International Journal of Bioinformatics Research and Application
Scopus
Biochemistry, Genetics and Molecular Biology; Medicine, Health

International Journal o f Data M ining and Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

IPSJ Transactions on Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Computer Science

Journal of Bioinformatics and Computational Biology
WoS & Scopus
COMPUTER SCIENCE

Journal of Clinical Bioinformatics
Scopus
Medicine

PLoS Computational Biology
WoS & Scopus
BIOLOGY & BIOCHEMISTRY

Reviews in Computational Chemistry
WoS & Scopus
CHEMISTRY

RSC Theoretical and Computational Chemistry Series
Scopus
Chemistry; Computer Science

Annual Reports in Computational Chemistry
Scopus
Chemistry; Mathematics

Computational and Structural Biotechnology Journal
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Computational and Theoretical Chemistry
WoS & Scopus
CHEMISTRY

COMPUTATIONAL BIOLOGY AND CHEMISTRY
WoS & Scopus
COMPUTER SCIENCE

COMPUTATIONAL CHEMISTRY
WoS
CHEMISTRY

Journal of Theoretical and Computational Chemistry
Scopus
Chemistry; Computer Science

Theoretical and Computational Chemistry
Scopus
Chemistry

Wiley Interdisciplinary Reviews: Computational Molecular Science
Scopus
Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics

Wiley Interdisciplinary Reviews- Computational Molecular Science
WoS
CHEMISTRY

Interdisciplinary sciences, computational life sciences
Scopus
Medicine

Interdisciplinary Sciences-Computational Life Science
WoS
Biology and Biochemistry

International Journal of Computational Biology and Drug Design
Scopus
Computer Science; Pharmacology, Toxicology and Pharmaceutics

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43926/aun-a-new-metric-to-measure-assembly-contiguity Tue, 02 Aug 2022 01:18:47 -0500 https://bioinformaticsonline.com/bookmarks/view/43926/aun-a-new-metric-to-measure-assembly-contiguity <![CDATA[auN: a new metric to measure assembly contiguity]]> Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A longer N50 indicates better contiguity. We can similarly define Nx such that contigs no shorter than Nx covers x% of the assembly. The Nx curve plots Nx as a function of x, where x is ranged from 0 to 100.

image

Address of the bookmark: https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter Fri, 12 Oct 2018 04:37:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter <![CDATA[DNA Nucleotide Counter]]> DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity Wed, 12 Dec 2018 08:36:08 -0600 https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity <![CDATA[OrthoANI: An improved algorithm and software for calculating average nucleotide identity]]> OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines. 

Address of the bookmark: https://www.ezbiocloud.net/tools/orthoani

]]> Abhimanyu Singh https://bioinformaticsonline.com/videolist/watch/4413/demo-4-using-blastblat-in-ensembl Tue, 10 Sep 2013 11:54:03 -0500 https://bioinformaticsonline.com/videolist/watch/4413/demo-4-using-blastblat-in-ensembl <![CDATA[Demo 4: Using BLAST/BLAT in Ensembl]]> We demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.]]> https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 Fri, 01 Jul 2016 12:09:59 -0500 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 <![CDATA[Genome Workbench 2.10.7]]> Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

  • BLAST Tool: added support for local custom BLAST databases
  • Graphical Sequence View: added log scaling option for graph tracks
  • Generic Table View: new tutorial added

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure
]]> Gudiya Pal