BOL: Related items

Bioinformatics JRF vacancy at ICGEB, New Delhi

Wed, 23 Jul 2014 16:07:15 -0500

Junior Research Fellow for a DBT sponsored project entitled "Computational and experimental characterization of stage specific arginine methylation in P. falciparum proteome".

Candidates should have a 1st class MSc/MTech/BTech degree in Bioinformatics. Please send complete CV, quoting Application for RMETH-JRF-2014, by email to Dr. Dinesh Gupta: dinesh@icgeb.res.in

Closing date for applications: 6 August 2014

More at http://www.icgeb.org/tl_files/Vacancies/JRF.pdf

Modern Statistics with R

LEGE — Thu, 22 Aug 2024 04:44:06 -0500

This is the online version of the second edition of Modern Statistics with R. It is free to use, and always will be. Printed copies are available from CRC Press.

Live online courses on statistics with R based on this book, led by the author, are offered regularly; see this page for more information and dates.

The past decades have transformed the world of statistical data analysis, with new methods, new types of data, and new computational tools. The aim of Modern Statistics with R is to introduce you to key parts of the modern statistical toolkit. It teaches you:

Data wrangling - importing, formatting, reshaping, merging, and filtering data in R.
Exploratory data analysis - using visualisations and multivariate techniques to explore datasets.
Statistical inference - modern methods for testing hypotheses and computing confidence intervals.
Predictive modelling - regression models and machine learning methods for prediction, classification, and forecasting.
Simulation - using simulation techniques for sample size computations and evaluations of statistical methods.
Ethics in statistics - ethical issues and good statistical practice.
R programming - writing code that is fast, readable, and (hopefully!) free from bugs.

The book includes plenty of examples and more than 200 exercises with worked solutions. The datasets used for the examples and the exercises can be downloaded here.

Address of the bookmark: https://www.modernstatisticswithr.com/

Linux Sort Commands for Bioinformatics

Rahul Nayak — Sat, 31 May 2014 15:41:16 -0500

Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

man sort

or

sort --help

on your Unix/Linux system.

Pangolin tutorial !

Abhi — Fri, 10 Dec 2021 05:58:59 -0600

This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page.

https://cov-lineages.org/resources/pangolin/tutorial.html

Address of the bookmark: https://cov-lineages.org/resources/pangolin/tutorial.html

Next generation sequencing in R or bioconductor environment

John Parker — Mon, 02 Jun 2014 18:03:09 -0500

There are many R software and bioconductor packages for NGS data analysis, some of them are as follows

Biostrings

The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers, string matching algorithms, and other utilities, for fast manipulation of large sets of biological sequences. The objects and functions provided by Biostrings form the basis for many other sequence analysis packages. Documentation

IRanges Overview

IRanges provides the low-level infrastructure and containers for handling sets of integer ranges within Bioconductor's BioC-Seq domain. Its classes and methods provide support for many more high-level packages like GenomicRanges, ShortRead, Rsamtools, etc. Documentation

GenomicRanges Overview

The GenomicRanges package serves as the foundation for representing genomic locations within the Bioconductor project. It is built upon the IRanges infrastructure and defines three major data containers - GRanges, GRangesList and GappedAlignments - which are supporting other important BioC-Seq packages including ShortRead, Rsamtools, rtracklayer, GenomicFeatures and BSgenome. Compared to the IRanges container, the GRanges/GRangesList classes are more flexible and extensible to store additional information about sequence ranges, such as chromosome identifiers (sequence space), strand information and annotation data. Documentation

Motif Discovery

cosmo

The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. Documentation

BCRANK

BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be applied to any ranked list of DNA sequences. Documentation

rGADEM: Documentation

MotIV: Documentation

ShortRead

The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. Documentation

Rsamtools

Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. Documentation

Samtools Website
BWA (Burrows-Wheeler Alignment) Website

Additional tools for SNP analysis:

snpMatrix

BSgenome

BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. Documentation

rtracklayer

rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. Documentation

biomaRt

The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. Documentation

ChIP-Seq Analysis Packages

Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: BioC ChIP-seq Case Study and BioC ChIP-Seq.

chipseq

The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. Documentation

BayesPeak

BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. Documentation [ Publication ]

PICS

The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. Documentation [ Publication ]

ChIPpeakAnno

The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. Documentation

Additional ChIP-Seq Packages

DiffBind: Documentation

MOSAICS: Documentation

iSeq: Documentation

ChIPseqR: Documentation

ChiPsim: Documentation

CSAR: Documentation

ChIP-Seq Pipeline: PICS, rGADEM and MotIV (developer web site)

SPP: ChIP-seq processing pipeline

SPP Tutorial

MACS

SIPeS

RNA-Seq Analysis

Counting Reads that Overlap with Annotation Ranges

The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are countOverlaps and summarizeOverlaps. For their proper usage, it is important to read the corresponding PDF manual. Documentation

Differential Gene Expression Analysis with DESeq

The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns). Such a count table can be imported into R or generated from BAM alignment files using the countOverlaps function as introduced above. Documentation

Differential Gene Expression Analysis with edgeR

The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data.

Documentation

A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG):

easyRNASeq (simplifies read counting per genome feature)

DEXSeq (Inference of differential exon usage); parathyroidSE explains how to generate exon read counts in R

DEGseq

baySeq (also see: segmentSeq)

Genominator (Bullard et al. 2010)

Detection of Alternative Splice Junctions

Another utility of RNA-Seq experiments is the analysis of splice junctions. The following software suggestions provide this utility:

ERANGE
TopHat

SpliceMap

SplitSeek

DNA-Methylation Data Analysis

methylPipe
bsseq
BiSeq
Much more under BiocViews

HT-Seq Data Visualization

ggbio: ggplot2 extension for genomics data (online manual) Gviz: Plotting data and annotation information along genomic coordinates HilbertVis: Hilbert genome plots

GenomeGraphs: Plotting genomic information from Ensembl

TileQC: Flow Cell Quality Visualization

rtracklayer: R interface to genome browsers

genoPlotR: Plotting maps of genes and genomes

Genominator: Tools for storing, accessing, analyzing and visualizing genomic data.

To install all packages

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))

Bioinformatics Courses Around the World

Jitendra Narayan — Fri, 19 Jul 2013 02:43:46 -0500

Bioinformatics Courses around the world

Here is the list Bioinformatics courses offered around the world. Reasons for constructing this page are:

To show the extent of growth of this new discipline
To provide a resource for students, and academics and
To access notes on the subject to allow some brief comparisons between courses.

The graduate courses outlined in the table mainly exist as a coursework component of an MSc or PhD degree. Of course, many institutions will also have pure research programs in Bioinformatics at the Hons, MSc, or PhD level and will not have a 'coursework component'. These research programs may not always reflect the main research program of the institution since the research depends upon the interests of a particular individual or small team within that institution. It is difficult to track these individual research programs. Consequently, we have not included all institutions with a bioinformatics research project. Bioinformatics is an interdisciplinary subject and this is reflected in the fact that the courses are offered by departments or schools as diverse as: computer science, biochemistry, molecular biology, microbiology, engineering, and mathematics. Similarly, bioinformatics may also be known by other names such as: computational biology, biocomputing, molecular informatics, computational molecular biology, biological information theory, molecular phylogenetics, and molecular bioinformatics.

Bioinformatics University Courses

Baylor College of Medicine, USA Ph.D. in structural and computational biology and molecular biophysics
Boston University, USA M.S. and Ph.D. program in bioinformatics
Carnegie Mellon, USA B.S., M.S. and Ph.D. Merck Computational Biology and Chemistry Program
George Mason University, USA M.S. and Ph.D. in bioinformatics and computational biology
Georgia Institute of Technology, USA M.S. in bioinformatics; Ph.D. in Bioinformatics and Computational Biology
Indiana University, USA B.S. and M.S. in informatics
Iowa State University, USA Ph.D. program in bioinformatics and computational biology
Johns Hopkins University, USA Ph.D. program in computational biophysics
Keck Graduate Institute, USA M.S. and Ph.D. in Bioinformatics and Computational Biology
Marquette University/MCW, USA M.S. in bioinformatics
New Jersey Institute of Technology M.S. and Ph.D. in Computational Biology
North Carolina State University, USA M.S. and Ph.D. in bioinformatics
Northern Illinois University, USA M.S. specialization in bioinformatics
Northeastern University, USA M.S. in bioinformatics
OHIO State University, USA Graduate Program in Biomedical Informatics
Rensselaer Polytechnic Institute, USA B.S. in bioinformatics and molecular biology
Rutgers University, USA Ph.D. in computational molecular biology
Stanford University, USA M.S. and Ph.D. in biomedical informatics
University of Medicine & Dentistry of New Jersey, USA M.S. and Ph.D. program in biomedial informatics
University of Medicine & Dentistry of New Jersey, USA M.S. and Ph.D. Bioinformatics track
University of Albany, USA Ph.D. program in comparative functional genomics
University of California, Irvine, USA M.S. and Ph.D Informatics in Biology and Medicine
University of California, Los Angeles, USA M.S. and Ph.D. program in bioinformatics
University of California, Santa Cruz, USA B.S., M.S. and Ph.D. in Bioinformatics
University of California, San Diego, USA Ph.D. Bioinformatics
University of California, San Francisco, uSA M.S. and Ph.D. program in biological and medical informatics
University of Cincinnati, USA M.S. and Ph.D. Biomedical Engineering-Bioinformatics track
University of Illinois, Chicago, USA M.S. & Ph.D. Bioinformatics
University of Memphis, USA M.S. concentration in bioinformatics
University of Michigan, Ann Arbor, USA M.S. & Ph.D. Bioinformatics
University of Minnesota, USA M.S. & Ph.D. Bioinformatics
University of Nebraska, Omaha, USA M.S. and Ph.D. in Bioinformatics
University of North Carolina, USA M.S. & Ph.D. Bioinformatics and Computational Biology
University of Pennsylvania, USA B.S., M.S. and Ph.D. programs in Computational Biology/Bioinformatics
University of Pittsburgh, USA M.S. and Ph.D. in bioimedical informatics
University of the Sciences in Philadelphia, USA B.S. in bioinformatics
University of the Sciences in Philadelphia, USA M.S. in bioinformatics
University of Southern California, USA M.S. & Ph.D. in Molecular and Computational Biology
University of Texas at Austin, USA Ph.D. in Cell and Molecular Biology-Structural Biology and Bioinformatics track
University of Texas at El Paso, USA M.S. in bioinformatics
University of Washington, Seattle, USA Ph.D. Graduate program in computational molecular biology
University of Wisconsin-Madison, USA Graduate Certificate in Bioinformatics
University of Wisconsin-Parkside, USA B.S. Molecular Biology & Bioinformatics; M.S. Applied Molecular Biology
Virgina Tech, USA Graduate program in bioinformatics
Washington University St Louis, USA Graduate program in computational biology
Centro de Ingenieria Geneticay Biotecnologia , Cuba
one week course
introductionto bioinformatic, June 21-25, 1999
(Universidad ) Nacional de General San Martin, Argentina
Instituto de Investigaciones Biotecnologicas
introduccion a la bioinformatica

Canada

Bioinformatics Training Program for Health Research (M.Sc. or Ph.D. in Bioinformatics)
Seneca College, Toronto (post-graduate diploma in Bioinformatics)
University of Toronto (Program in Proteomics and BioInformatics)
Simon Fraser University
University of British Columbia
University of Victoria
University of Alberta
The University of Calgary, Faculty of Medicine, The O'Brien Centre offers Bachelor of Health Sciences program (BHSc) in Bioinformatics
University of Lethbridge
University of Saskatchewan
University of Manitoba
Brock University
Carleton University
McMaster University
Queen's University
University of Guelph
University of Ottawa
University of Toronto
University of Waterloo offers Undergraduate research in Bioinformatics
University of Western Ontario
Wilfrid Laurier University
York University
Concordia University
McGill University
Université de Montréal
Mount Allison University
University of New Brunswick
Dalhousie University
University of Prince Edward Island
Memorial University of Newfoundlan

Europe

Birkbeck College, University of London (Accredited online course in protein structure) M.Sc. in molecular modelling and bioinformatics
Cranfield Centre for Bioinformatics and IT - MSc. Bioinformatics
Oxford University - Part-time MSc. in Bioinformatics
University of Abertay Dundee, UK Information Technology (Bioinformatics) - PGDip/MSc
University of Exeter - MSc, Diploma and Certificate in BioinformaticsMSc/MRes/PgDip/PgCert in Bioinformatics
University of Leeds, M.Res. in Bioinformatics
University of Liverpool, M. Sc. in Biosystems and Informatics
University of Manchester, Masters Program M.Sc. in bioinformatics, distance learning
University of Nottingham, Master of Philosophy in Molecular Biology with Bioinformatics
University of Wales College of Medicine, Cardiff, UK - Masters/Diploma/Postgraduate Certificate in Genetic Epidemiology and Bioinformatics
University of Glasgow, MRes in Bioinformatics
University of York, MRes in Bioinformatics
De Montfort University , MSc programme in Bioinformatics

Sweden

Uppsala University, Sweden (Basic courses)
University of Skovde, Sweden (MSc in bioinformatics)
Chalmers University Masters Program in Bioinformatics

Norway

University of Bergen, Norway (Masters-level courses)

Germany

Max Planck Institute for Molecular Genetics and Free University Berlin , PhD programs at the IMPRS-CBSC
Univ.of Bielefeld, Naturwissenschaftliche Informatik (Master's level course)
University of Tuebingen, Bioinformatics

Finland

Helsinki University, Graduate School in Computational Biology, Bioinformatics, and Biometry

France

Pasteur Institute (France) The bioinformatics courses at the Pasteur Institute are organized with the collaboration of the two largest Parisian scientific universities, Paris VI "Pierre et Marie Curie" and Paris VII "Denis Diderot". The diplomas delivered to students of these courses are considered equivalent to university degrees, for 1998 tuition of about 3 000 French Francs, or $500 US.
Université Montpellier II (IMGT Education - Immunoinformatics) (France)
Master's/PhD bioinformatique at Universite de Rennes
Master's/PhD Analyse de Génomes et Modélisation Moléculaire Université Paris
Master's/PhD "Application des Mathématiques et de l'Informatique à la Biologie" at Université d'Evry
Master's Bioinformatique at Université Paul Sabatier Toulouse
Master's/PhD bioinformatique de Bioinformatique et Genomique at Université Versailles St Quentin
Master's Pro Bioinformatique, Universite de Clermont-Ferrand
Master's Bioinformatique at Universite de Lille
Mastere Sciences, Mention: Bioinformatique, Biochimie Structurale et Génomique (BBSG) at Aix-Marseille University
(Universiteit) Amsterdam , Amsterdam, The Netherlands Centre for Integrative Bioinformatics
2-year International Masters in bioinformatics
(Univ of) Athens , Athens, Greece Bioinformatics postgraduate programme, Faculty of biology
http://bioinforMatics.biol.uoa.gr/msc/index-en.html
Semester A: 1. molecular biology & genomics; 2. biomolecular structure and function; 3. programming languages and software tools in bioinformatics (I); 4. statistics in bioinformatics; 5. principles and methods in bioinformatics; 6. application of informatics in the study and preservation of biodiversity.
Semester B: 1. computational analysis of biomacromolecular sequences; 2. computational analysis of biomacromolecular structures; 3. programming languages and software tools in bioinformatics (II); 4. molecular recognition - molecular diseases - structural drug design; 5. methodology of research.
Optional courses: 1. data types - databases - biological database design; 2. architecture of internet application and bioinformatics; 3. intelligent system techniques in bioinformatics; 4. complex adaptive systems; 5. special topics in bioinformatics.
Associazione Italiana Logica ed Applicazioni (AILA) , Italy
one time only,
11th International School for Computer Science Researchers: Computational Biology, June 20- July 3, 1999
(Universitat de) Barcelona and (Universitat) Pompau Fabra , Spain
Roderic Guigo, Enrique Blanco, Genis Parra, Sergi Castellano
a course on sequence analysis, a course on gene finding, a course on analysis of promoter region,...
master: bioinformatics for health sciences (2004-2005)
(Univ of) Bergen , Norway
Dept of Informatics,
I181 (Soking og maskinlaring)
KB207 (anvendt bioinformatikk), Fall 1999
(Universita di) Bologna , Italy
DEGREE: Laurea Specialistica in bioinformatics http://www.biocomp.unibo.it/lsbioinfo/
(Univ of) Buckingham , UK
Information Systems Department, plus Diabetes, Obesity and Metabolic Research Lab
MSc program on bioinformatics
(Univ of) Cambridge , UK MPhil in Computational Biology
Chalmers Univ (and Goteborg Univ), Sweden
Math,
MSN48, bioinformatics for biologists; MSN54, second course in bioinformatics; MSN56, population genetics; MSN55, statistical genetics
Cranfield Univ , Silsoe, UK
Centre for Bioinformatics & IT
MSc in bioinformatics
De Montfort University, UK
Bioinformatics MSc program 2003/2004
Dublin City University, Dublin, Ireland MSs in bioinformatics
Eidgenossische Technische Hochschule Zurich
Gina Cannarozzi
37-524 (computational biology), Oct 2000 - Feb 2001
Lars Ellgaard
01-327 (introduction to bioinformatics)
European Molecular Biology Network - Italian Node , Consiglio Nazionale delle Ricerche (CNR), Bari, Italy
David Judge, James Bonfield, three-day course
Sequencing Project Management Using the Staden package, September 20 - 22, 1999
European Molecular Biology Network - Swiss Node , Switzerland
one-week course
introduction to sequence analysis, Sept 2000
European Genetic Foundation , Bologna, Italy one-week courses
5th course in bioinformatics (Mar 20-24, 2005)
4th course in bioinformatics for functional genomics (March 26-30, 2004)
3rd course in bioinformatics (Aug 24-28, 2002)
2rd course in bioinformatics (Nov 14-18, 2001)
1st course in bioinformatics (Oct 22-26, 2000)
European Science Foundation , UK and other european countries
various
European School of Genetic Medicine, Italy
8th course in Bioinformatics & Systems Biology for Molecular Biologists, Bertinoro di Romagna, Italy, 16-20 May, 2008.
Exeter Univ, UK
School of Engineering and Computer Science and School of Biological Sciences, Postgraduate Programmes in Bioinformatics (E594/D594/C594)
BIO6201 (generic and transferable skills for bioinformatics), BIO6202 (bioinformatics tools and techniques), BIO6203 (biological sequence analysis and structural bioinformatics), BIO6204 (machine learning techniques in bioinformatics), BIO6205 (information systems for bioinformatics), BIO6206 (biotechnology and bioethics), BIO6207 (masters research project in bioinformatics), BIO6208 (diploma research project).
Free Univ Berlin Germany
Steffen Schulze-Kremer
Molekulare Bioinformatik, Summer 1993; Winter 1993-94 ; Summer 1995
(Univ of) Geneva , Swiss Institute of Bioinformatics, and (Univ of) Lausanne , Switzerland
Diplome d'etudes approfondies (DEA) plurifacultaire en Bioinformatique
(Univ of) Glasgow , Glasgow, Scottland, UK
Institute of Biomedical and Life Sciences
Master of Research (MRes) in bioinformatics (another page)
Graz Univ of Technology, Austria
Bioinformatics group of Institute of Biomedical Engineering
445.037, 445.038 (bioinformatics)
(Instituto) Gulbenkian de Ciencia , Portugal bioinformatics training courses ( several weekly course per year)
(Univ of) Helsinki , Helsinki, Finland
DEGREE: Master in bioinformatics http://www.cs.helsinki.fi/bioinformatiikka/mbi/
DEGREE: Ph.D program in computational biology, bioinformatics, and biometryhttp://www.cs.helsinki.fi/combi/
Human Genome Mapping Project Resource Centre , UK
2-3 days course
introductory biocomputing course, 2000; 1999 ;
gene ID and protain analysis, 2000; June 1999 ;
sequencing project management, 2000; 1999 ;
protein structure prediction, 2000; Nov 1999 ;
ACEDB workshop, 2000
Humboldt Univ Berlin , Germany
H Herzel, J Schuchhardt
G-31163 (introduction to bioinformatics), winter 1999-2000
Imperial College , London, UK
MC Field, Director
MSc in bioinformatics
International Centre for Genetic Engineering and Biotechnology , Trieste, Italy
Sandor Pongor, organizer (one week course)
bioinformatics: computer methods in molecular biology, Sept 1-6, 1997; July 3-10, 1998; 9-16 July 1999 ; june 30 -july 7, 2000
International Max Planck Research School for Computational Biology and Scientific Computing , Berlin, Germany http://www.imprs-cbsc.mpg.de/
3-year Ph.D program starting in October.
Karolinkska Institute , Sweden
Niclas Jareborg, Bill Wilson, Pia Jorgensen (one week course)
biomedicin - bioinformatics course;
bioinformatics, May 1999
Introduktion till bioinformatik, Jan-Feb 1999
Katholieke Universiteit Leuven , Leuven, Belgium master of bioinformatics
King's College London , UK
DEGREE: MSc/PG, PhD http://www.kcl.ac.uk/schools/pse/bioinform/
(Univ of) Leeds , UK
Master in Research in bioinformatics ,
BIOL5020M (bioinformatics of protein sequence, structure and function); BIOL5030M (bioinformatics project) BIOL5010M (bioinformatics programming (1)); BIOL5120M (bioinformatics programming (2)); BIOL5160M (bioinformatics of transcriptomic and proteomics); BIOL5170M (advanced options in bioinformatics and computational biology);
online MSc Bioinformatics program
(Univ of) Libre de Bruxelles , Belgium
Univ Libre de Bruxelles (ULB) plus 4 other universities: Facultes Univ Notre-Dame de la Paix(FUNDP), Univ de Liege (ULG), Univ Catholique de Louvain (UCL), and Univ de Mons-Hainaut (UMH), jointly organize a master program in bioinformatics
course (fall, 2000)
(Universidade de) Lisboa, Faculdade de Ciencias da (Faculty of Sciences of the University of Lisbon), Portugal post-graduate programme in bioinformatics (certificate, one year)
Ludwig-Maximilians-Universitat , Germany bachelor in bioinformatics
(Univ) Manchester, UK
Bioinformatics Unit
BS5061 (bioinformatics I), BS5072 (bioinformatics II), BS6220 (theory and algorithms in bioinformatics), BS5092 (biocomputing)
(Uni de la) Mediterannee , Marseille, France
Daniel Gauthret
bioinformatique, 2000
National University of Ireland , Maynooth, Ireland
EMBO Bioinformatics Workshop (June 25 - July 1, 2001)
undergraduate degree in computational biology and bioinformatics
bioinformatics summer school 2002
(Univ of) Nijmegen , Nijmegen, The Netherlands
Centre for Molecular and Biomolecular Informatics,
Bioinformatics 1,2,3,4,5
introduction to bioinformatics, aug 18-29, 2003
Norges Teknisk-Naturvitenskapelige Universitet , Norway bioinformatics program
Oxford Univ , UK
Bioinformatics Centre , School of Pathology
OUBC training courses
Part-time Modular MSc in Bioinformatics and regular short professional updating courses, Continuing Professional Development Centre, Oxford Programme in Biosciences
introduction to bioinformatics, three-day course, TBA
mining the knowledge of the new genomes, two-day course, TBA
algorithm design, one-week course, TBA
microarray bioinformatics, july 1-7, 2002; nov 25-29, 2002
genome analysis, nov 18-21, 2002
Pasteur Institute , France
various courses on informatics in biology, Jan-Apr, 2000
Royal Holloway, University of London , UK
MSc in computational biology for genomics and proteomics
(Universite de) Rouen , France
DEGREE: Master professionel de Bioinformatique http://www.univ-rouen.fr/ABISS/MasterBioinfo/
(Universitat des) Saarlandes , Germany
DEGREE: B.S. http://www.uni-saarland.de/de/studium/studienangebot/bioinformatik/
DEGREE: Master of science http://www.uni-saarland.de/de/studium/stud_int/englisch/bioinformatik/ http://www.uni-saarland.de/de/studium/studienangebot/angebot_abschluss/master/bioinformatik/
COURSE : http://zbi-www.bioinf.uni-sb.de/teaching/courses
(Univ of) Skovde , Sweden
CS
DEGREE: (one year) Master http://his.se/bioinformatics
Stockholm Univ , Sweden
Arne Elofsson,
structural biochemistry and bioinformatics, oct 1999-jan 2000;
bioinformatics, may-june 1999
Technical Univ of Denmark , Denmark
Steen Knudsen, Geeske de Witte Vestergaard
Center for Biological Sequence Analysis courses
(Univ of) Ulster F137PC: MSc bioinformatics
F536PC: PG Dip bioinformatics F138PC: PG Dip bioinformatics
Uppsala Univ , Sweden
Mats Gustafsson, Helena Danielson, Gerard Kleywegt
990304 (molecular bioinformatics), 2000, 1999 ;
Linnaeus Centre for Bioinformatics
bioinformatics, aug-oct 1999 ;
basics of bioinformatics ;
distance course in bioinformatics, 1999;
EMBO practical course: from genome sequences to protein structures, 1999
(Universiteit) Utrecht , The Netherlands Msc program in theoretical biology and bioinformaticcs
(Univ of) Valencia, Spain
Andres Moya Simarro, Fernando Gonzalez Candelas
Curso nacional de bioinformatica y biocomputacion,
Fernando Gonzalez Candelas
Analisis de secuencias de acidos nucleicos, 1997-1998
(Univ of) Wales College of Medicine, UK MSc/Postgraduate Diploma/Postgraduate Certificate (bioinformatics, genetic epidemiology and bioinformatics)
(Univ of) York , UK
DEGREE: Master of Research in Computational Biology,http://www.york.ac.uk/biology/masters/cb

Denmark

Belgium

Inter-University DEA/DES (Masters program in Bioinformatics)
Katholieke Universitiet (Masters program in Bioinformatics)

Switzerland

Swiss Institute of Bioinformatics (Masters program)

Austria

Bioinformatics at the Institute of Biomedical Engineering, Graz University of Technology

Israel

Weizmann Institute (Online course materials)

New Zealand

University of Auckland, New Zealand (BSc (Hons) in bioinformatics)
(Univ of) Otago , New Zealand
DEGREE: Bioinformatics is not at present taught as a separate degree course, but as integral components of other courses in Biology. Mathematics, Computer and Information Sciences
http://mrna.otago.ac.nz/Bioinfo/Bioinfo_teaching.html
Massey University, New Zealand
DEGREE: Bachelor of Science (Bioinformatics)
(Univ of) Auckland , Auckland, New Zealand
INSTITUTE: http://www.bioinformatics.org.nz/

Australia

La Trobe University (Basic course)
University of Melbourne (Bioinformatics stream within BSc degree)
University of Otago - Dunedin, New Zealand (Basic courses)
University of Queensland (3rd-year course)
University of Sydney (BSc program)
University of New South Wales (Bachelor of Engineering in Bioinformatics Programme)
Flinders University (Bachelor's Programme in Bioinformatics)
Australian National University , Canberra, Australia
DEGREE: Bachelor of Computer Science with a BioInformatics Emphasishttp://wwwmaths.anu.edu.au/study/bcomptlsci/bioinformatics.html
Central Queensland University , Rockhampton, Australia
DEGREE: Bachelor of Information Technology (Bioinformatics)http://handbook.cqu.edu.au/Handbook/programs_2.jsp?s=2&code=CQ08
Curtin University of Technology , Perth, Australia
DEGREE: Graduate Certificate in Applied Bioinformaticshttp://handbook.curtin.edu.au/courses/30/301135.html
Flinders Univ , Adeliade, Australia
DEGREE: Bachelor of Science in Bioinformatics and Molecular Biology (no new students in 2006) http://www.flinders.edu.au/calendar/vol2/ug/BScBioinf.htm CA Abbott
BINF 2201 (bioinformatics 2)
La Trobe University , Latrobe, Australia
DEGREE: Bachelor of Bioinformatics/Bachelor of Sciencehttp://www.latrobe.edu.au/biochemistry/bioinformatics/index.html
DEGREE: Master of Biotechnology and Bioinformaticshttp://www.latrobe.edu.au/biochemistry/mastersinbiotech/index.html
(Univ of) Melbourne, Melbourne, Australia
DEGREE: BCs with concentration in Bioinformaticshttp://www.cs.mu.oz.au/courses/ugrad/bcsbioinf.html
(Univ of) Queensland , Australia
DEGREE: Bioinformatics in the Bachelor of Biotechnologyhttp://www.uq.edu.au/study/plan.html?acad_plan=BIOINX2055
RMIT University , Melbourne, Australia
(Univ of) Southern Queensland Australia
DEGREE: Bachelor of BioInformatics
(Univ of) Western Australia , Australia
DEGREE: Bachelor of Science (Informatics)
(Univ of) Wollongong , Australia
DEGREE: Bachelor of Computer Bioinformatics

Asia & South Pacific

BioInformatics Institute, Singapore (Masters program)
National University of Singapore (Training and workshops)
Nanyang Technological University, Singapore (Master of Science in Bioinformatics)
National Tsing Hua University, Taiwan (Undergraduate course)
University of Hong Kong (Bachelor of Science in Bioinformatics)
University of Malaya, Malaysia (offers BSc & Msc in Bioinformatics)
Kebangsaan University, Malaysia (offers Bachelors of Science (Honours) in Bioinformatics)
Mohammad Ali Jinnah University, Pakistan (offers Bachelor of Science in Bioinformatics)
COMSATS Institute of Technology, Pakistan (offers Bachelor of Science in Bioinformatics)
GC University Faisalabad, Pakistan (offers Bachelor of Science in Bioinformatics)- Thanks Rabeea Rasheed
Academia Sinica , Taiwan Taiwan International Graduate Program: bioinformatics program
Amrita Vishwa Vidya Peetham (Deemed University) , India M.S. in bioinformatics
Chinese University of Hong Kong , Hong Kong, China
Dept of Biology
BIO4330 (bioinformatics and proteomics)
Beijing Univ, Beijing, China
(supported by International Centre for Genetic Engineering and Biotechnology)
Xiaocheng Gu, Jingchu Luo, Sandor Ponger, one-week course
molecular biology database and analysis tools, April 6-12, 1999 (broken link)
Introduction to bioinformatics, XiaMen University, Jul 23- Aug 3, 2001.
COURSE : Jingchu Luo: http://abc.cbi.pku.edu.cn/
Huaiqiu Zhu: http://ctb.pku.edu.cn/main/Course.htm
Bioinformatics Institute , Singapore
MSc in bioinformatics
Bioinformatics Institute of India, India
homepage
COMSATS Institute of Information Technology , Pakistan bachelor of science in bioinformatics
(The) Global Open University at Nagaland, India
DEGREE: M. Phil in Bioinformatics
http://nagaland.net.in/new_page_4.htm
(Univ of) Hong Kong , Hong Kong, China
DEGREE: Bachelor of Science in Bioinformatics http://www.hku.hk/bruhk/bscbioinf.htmljoint degree program by Dept of Biochemistry and Dept of Computer Science and Information.
Indian Institute of Chemical Technology ,Tarnaka, Hyderabad, India
advanced diploma in bioinformatics
Indian Institute of Information Technology , Allahabad, India
COURSES: http://bi.iiita.ac.in/
DEGREES: Master of Technology (BioInformatics) http://iiita.ac.in/inner.php?conf=grad
Institute of Bioinformatics and Applied Biotechnology , Bangalore, India
post graduate diploma courses
Jawaharlal Nehru Univ , India
bioinformatics center
advanced diploma in bioinformatics
KAIST, South Korea Department of BioSystems
BiS531 (bioinformatics), BiS532 (bioinformatics laboratory)
Keio University, Shoman-Fujisawa campus, Japan graduate program in bioinformatics
course list (in Japanese)
Madurai Kamaraj university, India
Bioinformatics Centre , Dept of Biotechnology
Advanced Diploma Course in Bioinformatics
(University of) Malaya , Malaysia
COURSE : http://combi.um.edu.my/
Mohammad Ali Jinnah University , Pakistan bachelor of science in bioinformatics
Nanyang Technological University, Singapore School of Computer Engineering
DEGREE: MSs http://www.ntu.edu.sg/SCE/msc-bioinformatics-intro.asp
National Dong Hwa University , Taiwan bioinformatics program
National Taiwan Normal University , Taiwan bioinformatics program
National Tsing Hua Univ , Taiwan
JK Huang, PC Lyu
LS4643 (bioinformatics) ; LS5650 (biodatabase)
National University of Singapore , Singapore
COURSE : http://www.comp.nus.edu.sg/~wongls/bp/courses.html
National Yang Ming Univ , Taiwan
Ueng-Cheng Yang,
bioinformatics master program (in Chinese)
Pune Univ , India
AS Kolaskar, RR Joshi
BI101-105,201-205 (advanced diploma courses in bioinformatics)
St. Joseph's College of Information Technology and Management Studies, Kerala State, IndiaMaster of Science in Bio Informatics (M.Sc BI)

Africa

Rhodes University, South Africa offers an MSc. in Bioinformatics and Computational Molecular Biology
South African National Bioinformatics Institute (SANBI), offers an MSc. in Bioinformatics
Arab League Educational, Culture and Scientific Organisation , Egypt
Robert Harper, Alessio Giacomini, Fredj Tekaia, M Mansour
bioinformatics, Nov 27- Dec 3, 199?
Bionet Africa , Kenya training workshop on bioinformatics/computational biology, Sept 24-25, 2002
Centre de Biotechnologie de Sfax, Sfax, Tunisia
Bioinformatics and genome data analysis: March 24 - April 2, 2000
(Univ of) Ibadan , Nigeria
west African bioinformatics training course, May 26-June 7, 2003
(Institut) Pasteur Tunis, Tunisia
A Benkahla, F Tekaia, A Rebai, E Yeramian
Bioinformatics and Comparative Genome Analysis course, March 18-April 7, 2007
(Univ of) Sfax , Tunisia
F Tekaia, A Rebai, H Haj Kacem, S Abdelhak, N Louhichi, H Ayadi
introduction to bioinformatics, May 26-31, 2003
(Univ of) Western Cape , South Africa
MSc and PhD programmes in Bioinformatics
Stanford/South Africa Bio-medical Informatics Programme
Winston Hide, South African National Bioinformatics Institute
introduction to bioinformatics
Regional training course on bioinformatics applied to tropical diseases In Africa , March 19 - April 4, 2003

Others:

(The) Hebrew University of Jerusalem , Jerusalem, Israel Hanah Margalit, Mol Genetics and Biotech
72677 (bioinformatics: computational sequence analysis of biological macromolecules)
67305 (research methods in computational biology)
Technion, Israel
Benny Chor, Computer Science (CS)
236606 (algorithms for computational biology), 1998
(Univ of) Tehran , Iran Iran Bioinformatics Center
International training course: computer application in molecular biology, September 7-13, 2002
Tel Aviv Univ , Israel
Ron Shamir, CS
0368-4137-01 (analysis of gene expression data, DNA chips and gene networks, Spring 2002 ,
0368.4020.01 (algorithms in molecular biology), Fall 1998
Racheli Kreisberg-Zakarin
Bioinformatics, Spring 2000
Weizmann Institute of Science, Israel
introductory computer course for the life sciences ;
Vered Chalifa-Caspi, Jaime Prilusky,
programming course for bioinformatics and internet (I) ;
Jaime Prilusky, Marilyn Safran,
programming course for bioinformatics and internet (II) ;
Gustavo Glusman, Michael Rebhan
bioinformatics & computational genomics, Spring 1998

Advanced Courses and Papers

BioInformatics Institute, Singapore (Ph.D Program)
Bibliography on Computational Gene Recognition (Rockefeller University)
Evaluating Regularizers for Estimating Distributions of Amino Acids (Paper by Kevin Karplus, UC Santa Cruz)
Iowa State University, PhD Program in Bioinformatics and Computatinal Biology (Ames, Iowa)
Perl Programing Course for Bioinformatics and Internet (Weizmann Institute of Science, Israel)
Rutgers University, PhD Program in Computational Biology (Newark, New Jersey)
Sequence Alignment and Modeling System (Documentation for SAM)
Technical University of Denmark, PhD Course in Biological Sequence Analysis and Protein Modeling
Training Program for Bioinformaticians in Health Research - Vancouver (M.Sc. and Ph.D. Programs)
University of Pennsylvania (Doctoral Program and Postdoctoral Program )
USC (PhD Program)
Virtual School of Natural Sciences (Online Courses)
De Montfort University, U.K, BioHealth Informatics research team offers MPhil and PhD studies in various computational biology and health related subjects

If your university is not there in the list, please let me know info_at_bioinformaticsonline.com

Postdoc position at Centre Méditerranéen de Médecine Moléculaire - Nice - France

Wed, 04 Jun 2014 07:20:57 -0500

The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.

Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Homepage: http://www.unice.fr/c3m/EN/Equipe10.html

One page R survival guide !!

Rahul Nayak — Thu, 28 May 2015 21:10:12 -0500

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 - *

Ten recommendations for creating usable bioinformatics command line software

RAJESH DETROJA — Sun, 08 Jun 2014 10:06:26 -0500

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

Bioinformatics algorithms tutorials

John Parker — Tue, 24 Jun 2014 00:10:45 -0500

Useful bioinformatics tutorial, such as

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/