<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/21444?offset=60 https://bioinformaticsonline.com/bookmarks/view/10182/biocodesbioscripts Tue, 22 Apr 2014 20:53:33 -0500 https://bioinformaticsonline.com/bookmarks/view/10182/biocodesbioscripts <![CDATA[BioCodes/BioScripts]]> Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

]]> Jit https://bioinformaticsonline.com/opportunity/view/10380/ra-at-alagappa-university Sun, 04 May 2014 23:33:15 -0500 <![CDATA[RA at ALAGAPPA UNIVERSITY]]> DEPARTMENT OF BIOTECHNOLOGY
(UGC SAP and DST-FIST & PURSE Sponsored Department)
ALAGAPPA UNIVERSITY
(A State University Accredited by NAAC with „A‟ Grade)
Karaikudi - 630 004, India

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

]]> https://bioinformaticsonline.com/opportunity/view/10459/associate-professor-bio-informatics-at-university-of-allahabad-in-allahabad Wed, 07 May 2014 00:26:53 -0500 <![CDATA[Associate Professor - Bio-Informatics at University of Allahabad in Allahabad]]> No of vacancies: 01

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

]]> https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation Sat, 10 May 2014 04:41:22 -0500 https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation <![CDATA[DNA Replication Process [3D Animation]]]> See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/]]> https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials Sat, 24 Aug 2013 06:01:37 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials <![CDATA[Next Generation Sequencing (NGS) Tutorials]]> Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/ 

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit. 

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

==============================================

NGS data analysis pipelines

  • Detecting and annotating genetic variations using the HugeSeq pipeline  DOI: 10.1038/nbt.2134
  • NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
  • RseqFlow: Workflows for RNA-Seq data analysis  DOI: 10.1093/bioinformatics/btr441
  • ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence  10.1186/1471-2164-12-285
  • A framework for variation discovery and genotyping using next-generation DNA sequencing data  PubMed: 21478889
  • SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects  DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
  • WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
  • DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
  • GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
  • Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
  • RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
  • Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
  • Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
  • Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
  • Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
  • RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ". 

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/

]]> Jitendra Narayan https://bioinformaticsonline.com/opportunity/view/10748/bioinformatics-phd-at-cuk-kerala Sat, 10 May 2014 20:21:22 -0500 <![CDATA[Bioinformatics PhD at CUK Kerala]]> Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;

1. Cancer Genomics

2. Microbial Genetics and Metagenomics

3. Human Infective Diseases

4. Computational Drug Design

Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor & Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com

]]> https://bioinformaticsonline.com/news/view/11144/scientists-map-17294-proteins-produced-in-human-body Thu, 29 May 2014 01:57:55 -0500 https://bioinformaticsonline.com/news/view/11144/scientists-map-17294-proteins-produced-in-human-body <![CDATA[Scientists map 17,294 proteins produced in human body]]> 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

 

]]> Jit https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel Fri, 30 May 2014 13:24:11 -0500 https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel <![CDATA[How to sequence the human genome - Mark J. Kiel]]> 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.]]> https://bioinformaticsonline.com/videolist/watch/11354/genomics-and-personalized-medicine Sun, 01 Jun 2014 23:38:42 -0500 https://bioinformaticsonline.com/videolist/watch/11354/genomics-and-personalized-medicine <![CDATA[Genomics and Personalized Medicine]]> (October 20, 2009) Michael Snyder, Professor of Genetics and Chair of the Department of Genetics at Stanford, discusses advances in gene sequencing, the impact of genomics on medicine, the potential for personalized medicine. and efforts at Stanford to further study these issues. Stanford Mini Med School is a series arranged and directed by Stanford's School of Medicine, and presented by the Stanford Continuing Studies program. Featuring more than thirty distinguished, faculty, scientists and physicians from Stanford's medical school, the series offers students a dynamic introduction to the world of human biology, health and disease, and the groundbreaking changes taking place in medical research and health care. Stanford University http://www.stanford.edu Stanford University School of Medicine http://med.stanford.edu Stanford Continuing Studies http://continuingstudies.stanford.edu Stanford University Channel on YouTube: http://www.youtube.com/stanford]]> https://bioinformaticsonline.com/blog/view/22454/one-page-r-survival-guide Thu, 28 May 2015 21:10:12 -0500 https://bioinformaticsonline.com/blog/view/22454/one-page-r-survival-guide <![CDATA[One page R survival guide !!]]> There any many of the documents have been developed and tested by scientist around the world. I found this one really useful. The data used is available for download as data.zip.

Reference@http://www.datasciencecentral.com/profiles/blogs/one-page-r-a-survival-guide-to-data-science-with-r

  • Templates for the Data Scientist
    1. A Template for Preparing Data: *OnePageR - *R
    2. A Template for Building Models: *OnePageR - *R
  • Getting Started as a Data Scientist
    1. Getting Started with R and Rattle: *Lecture - *Laboratory
    2. Introducing and Interacting with R: *Lecture - *Laboratory
    3. BasicR - OnePage(R) - Writing R scripts
  • Dealing With Data
    1. Read Data into R: *OnePageR - *R
    2. Explore and Summarise Data: *OnePageR - *R
    3. Transform Data: *OnePageR - *R
    4. Dealing with Dates and Time: (PDF, R) Dates and Time
    5. Visualising Data with GGPlot2: *OnePageR - *R
    6. Visualising Data with Maps *OnePageR - *R
    7. Spatial (R) Spatial Analysis
    8. Handling Big Data *OnePageR - *R
  • Descriptive Analytics
    1. Cluster Analysis: *Lecture - *OnePageR - *R
    2. Association Analysis: *Lecture
  • Predictive Analytics
    1. Decision Trees: *Lecture - *OnePageR - *R - *Rattle
    2. Ensembles of Decision Trees: *Lecture - *OnePageR - *R
    3. SVM (R)
    4. KernLab (R)
    5. NeuralNetworks (R)
    6. NNet (R)
  • Model Delivery
    1. Evaluating Models: *OnePageR - *R
    2. Evaluation (R)
    3. Scoring (R)
    4. PMML (R) Exporting Models for Deployment
  • Advanced Topics
    1. Text Mining: *OnePageR - *R
  • Advanced R Topics
    1. Plots (PDF, R) Miscellaneous Plots
    2. Functions (PDF, R) Writing Functions in R
    3. Parallel (PDF, R) Parallel Execution
    4. Packaging (R) Pulling it Together into a Package
    5. Doing R with Style: *OnePageR - *R
    6. Literate Data Mining with KnitR: *Lecture - *OnePageR - *
]]> Rahul Nayak