BOL: Related items

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

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.

A guide to machine learning for biologists

LEGE — Wed, 15 Sep 2021 13:21:08 -0500

We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to specific types of biological data, and also discuss some best practices and points to consider when one is embarking on experiments involving machine learning. Some emerging directions in machine learning methodology are also discussed.

Address of the bookmark: https://www.nature.com/articles/s41580-021-00407-0

Genomics and Personalized Medicine

Sun, 01 Jun 2014 23:38:42 -0500

(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

d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate the dissimilarity

Jit — Thu, 20 Sep 2018 08:38:29 -0500

d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively) measures. Hao, Dai, Eucliean, Mahattan, and Chebyshev distance measures are also included in d2Tools.

Manual at https://code.google.com/archive/p/d2-tools/wikis/d2ToolMannual.wiki

Address of the bookmark: https://code.google.com/archive/p/d2-tools/

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

Next Generation Sequencing (NGS) Tutorials

Jitendra Narayan — Sat, 24 Aug 2013 06:01:37 -0500

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/

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c

Tiny Python3.6 Notebook

Neel — Sat, 03 Jun 2017 03:16:28 -0500

This is not so much an instructional manual, but rather notes, tables, and examples for Python syntax. It was created by the author as an additional resource during training, meant to be distributed as a physical notebook. Participants (who favor the physical characteristics of dead tree material) could add their own notes, thoughts, and have a valuable reference of curated examples.

Address of the bookmark: https://github.com/mattharrison/Tiny-Python-3.6-Notebook/blob/master/python.rst

Bioinformatician’s Pocket Reference !!

RAJESH DETROJA — Sun, 08 Jun 2014 09:56:58 -0500

It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!

Address of the bookmark: http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/

BioStats class tutorial

Shruti Paniwala — Thu, 16 Mar 2017 01:50:50 -0500

Nice biostat turorial by Ingo Ruczinski

Address of the bookmark: http://www.biostat.jhsph.edu/~iruczins/teaching/