BOL: Related items

BIOINFORMATICS

Wed, 28 Aug 2013 19:16:33 -0500

This is a promo video for the brand new cross-boarder branch of study - BIOINFORMATICS. It´s a co-operation between Johannes Kepler University in Linz (Austria) and University of South Bohemia in České Budějovice (Czech Republic). Written, Edited and Directed by, DOP, VFX: Jan Míka Sound by: Mirek Šmilauer Narrator: Jack Bright Produced by: FILMOFON (http://www.filmofon.cz) Released: Nov 2012

Simpson Lab

Tue, 06 Mar 2018 08:59:09 -0600

We are the Statistical Bioinformatics group in the Institute for Adaptive and Neural Computation in the School of Informatics at the University of Edinburgh. The group is led by Dr. Ian Simpson who is a Lecturer in Biological Informatics in the School of Informatics at Edinburgh University. Details to follow....

http://statbio.github.io

Snakemake—a scalable bioinformatics workflow engine

Jit — Sun, 02 Sep 2018 16:32:42 -0500

Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.

Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

What is Bioinformatics?

Wed, 28 Aug 2013 06:53:05 -0500

Illustration and Animation: Rachel Robinson Script: Tiffany Trent Voice-over: Kris Monger Sound: Glisten Carefully by Guennadi Malyshevski

IBM Research Computational Biology Center

Thu, 29 Aug 2013 08:43:59 -0500

The IBM Computational Biology Center embraces activities at Yorktown Heights, with strong affiliations with activities at Almaden and other IBM Research Centers. Computational Biology (CompBio) including bioinformatics is the study of how computer systems can manage, analyze, and simulate the complex structures and processes inherent in living systems. CompBio Research at IBM spans pattern recognition in sequences, structures and processes, the studying of systems ranging from single protein molecules through to complex molecular interactions, and the data analysis, interpretation and reverse-engineering of complex disease-lifestyle-genomic interactions for fuller biological understanding. "CompBio" has a flavor of its own independant of its parents, biology and computer science. Nonetheless, CompBio is inherently a multi- disciplinary field with important applications in biology, chemical physics, materials science, agriculture, chemistry and ultimately nanotechnology.

Bioclues and Pine Biotech join forces to advance Bioinformatics in India

eliabrodsky — Fri, 14 Jun 2019 10:20:47 -0500

As a collaborative effort, the two organizations will help implement best practices in bioinformatics education across universities in Inida that have little to no experience in bioinformatics. The collaboration comes as Pine Biotech starts registrations for it's pilot program at Amity University in Kolkata, India.

To read more about this collaboration, visit: https://edu.t-bio.info/pine-biotech-joins-forces-with-the-bioclues-organization-to-promote-bioinformatics/

May 17, 2013 - Differential Network Analysis

Wed, 04 Sep 2013 16:22:28 -0500

Steve Horvath presents Differential Network Analysis at the UCLA Human Genetics/Biostatistics Network Course

Project Fellow @ Alagappa University

Sat, 07 Sep 2013 14:24:13 -0500

Advertisement for the post of project Fellow in UGC project

Project Fellow – One Post

Duration: Three Years

Fellowship : Rs.14, 000/- per month + HRA

Walk-in-interview: 16th Sept, 2013 at 10.00 am

Venue : Department of Bioinformatics, Alagappa University

Eligible candidates can attend walk in interview for the post of Project Fellow in UGC supported project entitled “Shape and chemical feature based 3D- Pharmacophore Model generation, Virtual Screening and MESP studies to identify Potential Leads for Antifungal Azoles”

Interested candidates may apply to Dr. Sanjeev Kumar Singh, Principal Investigator, Department of Bioinformatics, Karaikudi with their Curriculum Vitae along with the copies of the certificates in proof of their educational qualification and experience at skysanjeev@gmail.com

Qualification:

PG Degree in Bioinformatics / Chemistry/ Molecular Biology/ Biotechnology / Biophysics / Biochemistry / Life Sciences/ Pharmacy with minimum of 55% marks in the PG examinations

Desirable:

Research experience in Molecular modeling and CADD will be given preference. UGC-NET/ CSIR-JRF qualified candidates will get preference.

The posts are purely on temporary basis. No TA/DA will be paid for attending the interview.

Advertisement: http://www.alagappauniversity.ac.in/files/news_files/new%20advt-UGC-16sept,13.doc

NGSymposium in Computational Biology

Mon, 09 Mar 2020 06:00:30 -0500

We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

Frequent parameters for bioinformatics tools !

BioStar — Tue, 27 Oct 2020 19:42:32 -0500

Third party executable parameters and options.

Trimmomatic

“ILLUMINACLIP:...:2:30:10”

“LEADING:15”

“TRAILING:15”

“SLIDINGWINDOW:4:20”

“MINLEN:20”

“TOPHRED33”

Filtlong

--min_length 500

--min_mean_q 85

--min_window_q 65

FastQ Screen

--aligner bowtie2' (bwa for PacBio)

--subset 1000 (for PacBio)

SPAdes

--careful

--disable-gzip-output

--cov-cutoff auto

--phred-offset 33

HGAP

Pbalign.task_options.min_accuracy: 70

Pbalign.task_options.no_split_subreads: false

Genomic_consensus.task_options.min_confidence: 40

falcon_ns.task_options.HGAP_GenomeLength_str:

6000000

Pbcoretools.task_options.read_length: 0

Genomic_consensus.task_options.use_score: 0

Pbalign.task_options.min_length: 50

Pbalign.task_options.algorithm_options: --minMatch 12

--bestn 10 --minPctSimilarity 70.0

Pbalign.task_options.hit_policy: randombest

Pbcoretools.task_options.other_filters: rq >= 0.7

Pbalign.task_options.concordant: false

Genomic_consensus.task_options.min_coverage: 5

falcon_ns.task_options.HGAP_SeedCoverage_str: 30

falcon_ns.task_options.HGAP_AggressiveAsm_bool: false

Genomic_consensus.task_options.algorithm: best

falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1

Genomic_consensus.task_options.diploid: false

MeDuSa

-random 100

Prokka

--usegenus

--force

--addgenes

--rfam

--rawproduct

cmsearch (taxonomy, 16S)

--rfam

--noali

blastn (taxonomy, 16S)

-evalue 1E-10

blastn (MLST)

-ungapped

-dust no

-evalue 1E-20

-word_size 32

-culling_limit 2

-perc_identity 95

blastp (VF)

-culling_limit 2

RGI (ABR)

--input_type contig

bowtie2 (mapping)

--sensitive

minimap2 (mapping)

-a

-x map-ont

samtools mpileup (SNP detection)

-uRI

bcftools call (SNP detection)

--variants-only

--skip-variants indels

--output-type v

--ploidy 1

-c

SNPsift filter (SNP detection)

"( QUAL >= 30 ) & (( na FILTER ) | (FILTER = 'PASS')) &

( DP >= 20 ) & ( MQ >= 20 )"

SNPeff ann (SNP detection)

-nodownload

-no-intron

-no-downstream

-no SPLICE_SITE_REGION

-upDownStreamLen 250

bcftools consensus

(phylogenetic tree)

--haplotype 1

fasttreemp

-nt

-boot 100

roary

-e

-n

-cd 100

-g 100000