<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26975?offset=1130 https://bioinformaticsonline.com/opportunity/view/17187/urdip-bioinformatics-rajrf-vacancies Sat, 20 Sep 2014 20:52:56 -0500 <![CDATA[URDIP Bioinformatics RA/JRF Vacancies]]> CSIR - UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS (CSIR- URDIP)

Adv. No. URDIP/ 6/2014

Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.

The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.

CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.

Position I: Research Associate

No of Positions: One

Consolidated amount Payable: Rs. 22,000/- per month + 20% HRA= Rs.26,400

Qualification: PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.

Age Limit: 35 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.

Upper age limit is relaxable for 5 years for SC/ST, OBC, Physically handicapped and female candidates as per CSIR/Government of India rules.

Position II: Junior Research Fellow

No of Positions: one

Consolidated amount Payable: Rs. 16,000/- + 20% HRA = 19,200

Qualification: M.Sc / BE or equivalent in Bioinformatics with minimum of 55% marks in aggregate Job requirement: Scientific literature and patent search, analysis and Report Writing

Preference: Preference will be given to candidates with knowledge of patents and or 1-2 years of experience + Knowledge of Computers (MS Excel + Word Processing)

Age Limit: 28 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.

For details please visit our website (www.urdip.res.in/careers) for further details and apply online by 30th September, 2014.

Advertisement: http://www.urdip.res.in/download/Advt6_2014.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools Thu, 16 Jan 2020 23:14:00 -0600 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools <![CDATA[ngs-bits - Short-read sequencing tools]]> Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Address of the bookmark: https://github.com/imgag/ngs-bits

]]> Neel https://bioinformaticsonline.com/bookmarks/view/17176/arvados Sat, 20 Sep 2014 16:54:21 -0500 https://bioinformaticsonline.com/bookmarks/view/17176/arvados <![CDATA[Arvados]]> Arvados is a free and open source bioinformatics platform for genomic and biomedical data. User can Store | Organize | Compute | Share the data for free. 

image

Address of the bookmark: https://arvados.org/

]]> Martin Jones https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping Wed, 29 Jan 2020 06:29:55 -0600 https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping <![CDATA[Understanding your reads and mapping !]]> One of the best tutorial for beginners ...

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing Mon, 27 Nov 2017 10:38:56 -0600 https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing <![CDATA[INC-Seq: accurate single molecule reads using nanopore sequencing]]> INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

Address of the bookmark: https://github.com/CSB5/INC-Seq

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35883/arcs-scaffolding-genome-drafts-with-linked-reads Tue, 06 Mar 2018 16:35:26 -0600 https://bioinformaticsonline.com/bookmarks/view/35883/arcs-scaffolding-genome-drafts-with-linked-reads <![CDATA[ARCS: scaffolding genome drafts with linked reads]]> ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.

Address of the bookmark: https://github.com/bcgsc/ARCS/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads Tue, 08 May 2018 04:27:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads <![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]> HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). 

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/18819/jrfsrf-at-jawaharlal-nehru-institute-ofadvanced-studies-jnias-hyderabad Fri, 31 Oct 2014 08:48:23 -0500 <![CDATA[JRF/SRF at Jawaharlal Nehru Institute ofAdvanced Studies (JNIAS), Hyderabad]]> Applications for Academic Projects in Biotechnology, Bioinformatics, Environmental Sciences and Computer Science & Engineering

About JNIAS
Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D. Swaminadhan Research Foundation (DSRF), Hyderabad as a Research and Educational Institution with a view to contribute in developing advanced technologies and build „core competence‟ in specific areas. The activities of JNIAS involves: Education, Research Training and Innovations in the fields of Sciences, Technologies, Humanities and Social Sciences. It aims to blossom into an Advanced Institute of education and research with a reservoir of expertise and experience in the relevant fields and the necessary capability to harness multi-disciplinary research and studies. JNIAS has been recognized as an Advanced Research Institute by Jawaharlal Nehru Technological University Hyderabad (JNTUH), Hyderabad and Jawaharlal Nehru Technological University Anantapur (JNTUA), for offering Ph.D., P.G M.Phil, P.G Diploma and Training Programmes in Sciences and Engineering & Technology.

Jawaharlal Nehru Architecture and Fine Arts University (JNAFAU) Hyderabad also recognized JNIAS for offering UG, PG degree in Architecture.

Projects & Facilities

JNIAS offers wide range of projects:

Biotechnology area:

Molecular Biology
Microbiology
Nanotechnology
Bioinformatics (Schrodinger Software)
In Silico studies & Drug Designing
Sequence analysis
Protein structure function studies

Registration
Tuition Fees: Interested students need to pay the following tuition fees:
1. Six Month’s Project: Rs. 20,000/-
2. Four Month’s Project: Rs. 15,000/-
3. Three Month’s Project: Rs. 10,000/-
4. One Month - Hands on Training : Rs. 8,000/-

For enquires call:
91-7893203414 (Biotechnology), 91-9949582263 (Environmental Sciences) 91-8977369305 (Computer Science)

Interested student may download the application from the website (www.jnias.in) and send the hard copy of the completed application forms and Curriculum Vitae along with the Demand Draft drawn on any nationalized Banks in favor of “The Registrar, JNIAS, Secunderabad”. Application forms can be sent through email to academicprojects@jnias.in

Address
Jawaharlal Nehru Institute of Advanced Studies (JNIAS)
6th Floor, Buddha Bhavan, M.G Road,
Secunderabad - 500 003
Andhra Pradesh, India
Tele/Fax: 040- 27541551; 27541553
Mobile: 08885541554
Web site: www.jnias.in

Brochure : https://drive.google.com/file/d/0B3zPwhgA-u-nU0dyMFd2OWcxNUpSTWNYc0xDSGs5UDI4UDNB/view?usp=sharing

]]> https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads Tue, 15 May 2018 09:42:32 -0500 https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads <![CDATA[Circlator: automated circularization of genome assemblies using long sequencing reads]]> Address of the bookmark: http://sanger-pathogens.github.io/circlator/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics Fri, 17 Oct 2014 02:14:14 -0500 https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics <![CDATA[Google Genomics]]> Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.

  • Store alignments and variant calls for one genome or a million.
  • Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
  • Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
  • Share genomic data with your research group, collaborators, the broader community, or the public. You decide.

Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

]]> Reshma Khatun