BOL: Related items

PhD positions in Genova at DIBRIS - Univ. of Genoa, Italy

Thu, 18 May 2017 00:04:07 -0500

PhD positions in Genova at DIBRIS - Univ. of Genoa (Italy)

http://www.disi.unige.it/person/MasulliF/ricerca/PhDinGenova2017.html

The call for some funded positions for the 3 years PhD studies at the Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS) in Genova is available at

http://www.studenti.unige.it/postlaurea/dottorati/XXXIII/ENG/

The deadline for applications is June13, 2017 and the PhD courses and fellowships should start on Nov 2017.

Details for the application to the PhD Program in Computer Science and Systems Engineering (CODICE 6608) are at http://phd.dibris.unige.it/csse/index.php/how-to-apply

The research activity of my research group is focused on Computational Intelligence, Machine Learning, Bioinformatics, Systems Biology, and Positive Technology as described at http://www.disi.unige.it/person/MasulliF/ricerca/index.html

The research themes proposed by me and Prof. Stefano Rovetta are:

- Computational Intelligence and Machine Learning (see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T1.html)

- Computational Intelligence and Health and Wellbeing Support( see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T3.html)

You can also propose a different research theme belonging to the research activity of my group.

Looking for self-motivated PhD candidates, interested to the mathematical aspects of their research and to the development of new algorithms for intelligent data analysis, and skilled in programming and in thorough experimental data analysis. They will be part of my research group and will collaborate to our research projects and publications.

Italian and international students interested to work are invited to send their cv and the name/email-addresses of 3 referees to my email address francesco.masulli@unige.it A.S.A.P.

RA Bioinformatics at NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS, INDIA

Wed, 26 Jul 2017 03:49:52 -0500

NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS
(An Autonomous Institution of the Government of India)
P.O.: N.S.S., Kalyani 741251, West Bengal

Advertisement No. 137/ESTB/NIBMG/17-18

Position available Project Description: Several positions are available for the project titled: “A unified web-portal for analysis, integration and visualization of multi-omics data”. The goal of this project is to develop a user-accessible resource for integrated analysis and visualization of multi-OMICs data sets (including gene expression, genotype, methylation, microRNA, etc.). Data sets generated on various platforms shall be maintained in a stable database, accessed through standard querying mechanisms, and the results shall be displayed via user-friendly interface. The analysis engine shall run on open-source software (such as R/Bioconductor) developed in-house. All positions are contractual.

Appointment will be initially given for a period of one year which is extendable depending upon performance, availability of funds and requirements of the institute.

Project Code: 20275 Position: (No. of positions available)

Research Associate (3)

Position 1: Ph.D. or equivalent in statistics, computer science, mathematics, bioinformatics, or related subject.
Position 1: Those with experience in database management shall be preferred. Experience with UNIX or GNU/Linux operating system.
Position 1: Creation and maintenance of a database for population- and diseaseassociated variation resource. Development of programmatic interface for querying the database, filtering of the results and identification of genes of interest.

Rs. 36000/- + 10% HRA

Please apply online via web link http://apply.nibmg.ac.in/ (no other form of application will be accepted). The last date of application is 14-08-2017. All letters to attend screening test and /or interview will be sent only to the short-listed candidates by Email only. No correspondence will be made with applicants who are not shortlisted /not called for screening test and /or interview. No TA/DA will be paid for attending the screening test and /or interview.
Detail information at http://www.nibmg.ac.in/academic/Advt_20275.pdf

More Info: http://www.nibmg.ac.in/?q=Project%20Linked%20Personnel

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

Bioinformatics lectures !

Jit — Wed, 29 Nov 2017 05:39:54 -0600

Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to adjust as appropriate. However, here is a tentative list of topics I hope to cover this semester (not necessarily in order).

Optimal sequence alignment (global, local, and glocal alignment &mdash with constant & affine gap penalties
Algorithms and data structures for efficient text indexing and exact search
Heuristics for read alignment and mapping &mdash mapping DNA-seq and RNA-seq reads
Genome assembly &mdash k-mers, De Brujin graph construction and representation, long-read technology and read-overlap graph assembly
Motif finding via Gibbs sampling
Gene finding &mdash statistical models for ab initio and evidence-guided prediction of genes
RNA-seq and transcriptomics &mdash transcript assembly, abundance estimation and differential expression testing
Phylogenetics &mdash The small and large phylogeny problem; parsimony, maximum likelihood and Bayesian methods

Address of the bookmark: https://rob-p.github.io/CSE549F16/lectures/

SOAP2 : Short Oligonucleotide Analysis Package 2

Poonam Mahapatra — Wed, 23 May 2018 10:09:22 -0500

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Address of the bookmark: http://soap.genomics.org.cn/soapaligner.html

India and Germany to begin joint research in the area of 'Bioinformatics in Health Research'

Rahul Nayak — Wed, 17 Jan 2018 14:10:36 -0600

To facilitate bilateral cooperation in biotechnology between the scientific communities of India and Germany, the Department of Biotechnology (DBT) will soon begin collaborative research in the identified priority area of 'Bioinformatics in Health Research' under the programme of Indo-German Cooperation in Health Research.

The purpose of the programme is to stimulate new collaborations, e.g. the preparation of joint projects under national funding programmes. The programme facilitates bilateral cooperation in biotechnology between the scientific communities of India and Germany by way of joint research projects which will encompass bilateral workshops/seminar and exchange visits of scientists.

The programme is being implemented within the agreement of Indo-German cooperation in S&T of 1974, under which the Department of Biotechnology, Government of India and Forschungszentrum Julich BMBH (FZJ), Federal Republic of Germany, have agreed for cooperative programme in biotechnology.

DBT of the Ministry of Science & Technology, Government of India and the Project Management Agency at the German Aerospace Center (DLR-PT, European and International Cooperation), Bonn are the nodal implementing agencies from the Indian and German side respectively.

Through this programme, it is expected that the funded cooperation enables the partners to develop applicable scientific results which can be published and/ or could be commercialised and may lead to formation of joint ventures. All publications, patents coming out of these projects, need to be jointly authored by both Indian and German scientists. All necessary approvals like ethical clearance, HMSC approval from Indian point of view as well as EU, if applicable, from German point of view, e.g. before conducting animal experimentation if any needs to be obtained by PIs before undertaking the project.

Now, both the nodal agencies have invited research proposals in identified priority area of 'Bioinformatics in Health Research' from eligible scientists. Joint research projects are required to be submitted to both the nodal agencies by 15 January 2018. Scientists/faculty members working in regular capacity in universities, national R&D laboratories/institutes and private R&D institutes can be part of this joint research programme. For the private sector, partners from all kind of private sectors are eligible, but financing is limited. For Indian scientists from the private sector, only local hospitality in Germany as part of the exchange visit is available from the German side. For German scientists from the private sector, only travel costs are available for small and medium size enterprises (for definition of SME ref. to 2003/361/EC) as well as local hospitality in India will be borne by themselves.

RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models

Jit — Wed, 24 Oct 2018 22:38:05 -0500

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN

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

ShinyGO v0.61: Gene Ontology Enrichment Analysis + more

Jit — Wed, 03 Jun 2020 08:00:30 -0500

2/3/2020: Now published by Bioinformatics.

11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more.

5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db! Just paste your gene list to get enriched GO terms and othe pathways for over 315 plant and animal species, based on annotation from Ensembl (Release 96), Ensembl plants (R. 43) and Ensembl Metazoa (R. 43). An additional 2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs.

Address of the bookmark: http://bioinformatics.sdstate.edu/go/

BINC (Bioinformatics National Certification) Examination 2018

Jit — Mon, 23 Apr 2018 03:34:53 -0500

Bioinformatics National Certification (BINC) was instituted by Department of Biotechnology, Government of India in 2005 at Savitribai Phule Pune University, formerly University of Pune, Pune to certify bioinformatics professionals and recognizing candidate's theoretical and practical ability and fostering interdisciplinary research. Later on, it was transferred to Jawaharlal Nehru University, New Delhi and then to Pondicherry University, Puducherry. Pondicherry University conducted the BINC examination in 2015, 2016 and 2017.

Biotech Consortium India Limited (BCIL), New Delhi is conducting the BINC 2018 examination on behalf Department of Biotechnology, Government of India.

BINC is a certification programme for graduate and post-graduate students for recognizing their exceptional bioinformatics knowledge and skills and to improve their employment opportunities. There is a growing need for trained manpower in the area of Bioinformatics. Currently, various universities and institutions, both government and private, impart Bioinformatics education in India. The qualifying candidates will be awarded a lifetime certificate. This certification would facilitate industries and potential employers in recruitment of Bioinformatics professionals having exceptionally good bioinformatics skills.

The certification under Bioinformatics National Certification (BINC) scheme is given to the candidates after three tier selection process. The successful candidates are also eligible for availing Junior Research Fellowship (JRF) for pursuing Ph.D. in Bioinformatics at recognized Indian universities/institutes. The research fellowships of all BINC qualified Indian nationals are funded by DBT. BINC qualified candidates are called DBT certified Bioinformaticians while the individuals availing the fellowships are called as DBT-BINC Junior Research Fellows (DBT-BINC-JRF). Cash prize of 10,000/- each is awarded to the top 10 BINC qualifiers.

Eligibility

i) Bachelor's/Master's degree in Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences, Agriculture, Veterinary, Medicine, Pharmacy, Engineering and Technology.

ii) No formal training, diploma or certificate in bioinformatics is required.

iii) Candidates in final year of Bachelor's/ Master's degree are also eligible to apply.

Pattern of Examination

Syllabus

The syllabus consists of six sections - Bioinformatics, Biology, Physical Science, Chemical Science, Mathematics & Statistics, and Information Technology.

Note: Paper-III will be computer based practical and will include programming on Bioinformatics

Important Dates

Examination Centers

BINC Fellowship

Forms & Downloads

FAQs

Contact Us

Nisha Singh
Biotech Consortium India Limited
(CIN: U73100DL1990PLC041486)
5th Floor, Anuvrat Bhawan 210, Deen Dayal Upadhyaya Marg New Delhi - 110 002
Tel.: 011-2321 9064-67 Ext. 231, 236
Email - For general BINC queries:binc.dbt@biotech.co.in
Helpline for Application submission related queries:binchelpdesk@biotech.co.in
Website: www.bcil.nic.in/BINC.html