2013 Workshop on Genomics, Cesky Krumlov | Evolution and Genomics. An excellent series of blog posts about the 2013 Workshop on Genomics written by Melanie Melendrez from Walter Reed Army Institute of Research can be viewed on her site found here! T he 2013 Workshop on Genomics was held from 7-18 January, 2013 in Český Krumlov, Czech Republic. This will be the third time the Workshop will be held in Europe, and the fifth full-length Workshop on Genomics. A full schedule can be viewed below.
Modifications and additions to the schedule may be made at anytime prior to the beginning of the Workshop, however the overall content and structure will remain largely the same. The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop registration fee is $1800. Map of important locations: Workshop Guide. Information from the Infocentrum about activities, dining and other information can be found here.
Software - Bioinformatics Team (BioITeam) at the University of Texas. Software The following is a categorized list of software available through the UT GSAF and/or TACC's life sciences group. Each page lists a summary of the software, the hardware it is currently installed on, links to user documentation, and helpful tips. Many of these are available via the TACC module system (use module keyword or module spider to search). The current listing of modules and versions available on Lonestar is also posted here. In addition, the BioITeam maintains executables in /corral-repl/utexas/BioITeam/bin; we advise adding this directory to your path. Contents Galaxy Workflows General purpose tools Microarray data analysis tools MeV NGS Data Quality Control Tools Mappers/Aligners Gene prediction tools SNP discovery and Annotation RNA-Seq Analysis Splice Junction discovery Tophat- Cufflinks Genome Alignment and Visualization De novo assembly Transcriptome de novo assembly ABI pipelines Small RNA Pipeline 454 Analysis tools Current Roche/454 software versions on Fourierseq are all 2.5.3.
CodeSkulptor. LSHTM - Links for R. Guest Join | Help | Sign In LSHTM Home guest| Join | Help | Sign In Turn off "Getting Started" Loading... Join Now. CS 680 Homepage. Instructor: Christina Boucher Office: 344 Computer Science Building Office Hours: 10:45-noon on Thursdays or by request. Email: cboucher at cs.colostate dot edu Lecture Time and Place: 9:30-10:45 TR, CSB Room 425 The past decade has seen an explosion of biological data, including the DNA sequence of a number of organisms. News: Biostatistics 615/815: Main Page - Genome Analysis Wiki. Biostatistics 666: Main Page - Genome Analysis Wiki. Kevin's GATTACA World. Teaching - Oxford University Statistics. We teach computational biology, systems biology, comparative genomics and population genetics at DTC LSI and DTC Sysbio and MSc Bioinformatics, a 4th year course in the Department of Statistics and Comlab called 'Bioinformatics and Computational Biology. Lectures, exercises, practicals and projects can be downloaded from the corresponding webpages where, in the Dept Statistics, we have taught: Bioinformatics and Computational Biology The Analysis of Biological Networks Present Teaching 2008 February Gulbenkian course plan 2009 February Gulbenkian course plan 2009 February AIMS (Stellenbosch) course plan 2009 June Iceland course plan 2009 August BiRC Masters course course plan 2010 May OIST, Japan Furthermore, we are preparing a two week course course on Topics in Computational Biology.
Earlier Teaching Much of my teaching material was started when I taught at Birc for 10 years. I also taught Summer Institute in Statistical Genetics for 10 years, when it was at NCSU with Jeff Thorne. FASTX-Toolkit. Introduction The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others. However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.
Available Tools FASTQ-to-FASTA converterConvert FASTQ files to FASTA files. Tools demonstration Visit the Hannon lab public galaxy server to see a demonstration of these (and other) tools. News 02-Feb-2010 - Version 0.0.13 Dec-2009 - Version 0.0.12. Untitled. Bioinformatics challenges developers to create widely distributable tools that elucidate biological relationships. The principal value of these tools is measured in the contribution they provide to research biologists. Furthermore, as the amount and nature of available data increases, bioinformaticians are forced to provide rapidly evolving tools to their user communities. Java has allowed bioinformaticians to rapidly develop user-friendly, cross-platform applications that are accessible to users at all levels of computational ability. The creation of many new bioinformatic applications is largely a response to the biological community aggregating types of knowledge and developing new experimental techniques.
Genome browsers, like EnsEMBL and UCSC, actively aggregate and serve annotation for several genomes (the chemical sequences that make up an organism's DNA). The second bioinformatics task is primarily concerned with determining the structure and function of genomic sequences. Train online | EBI Train online. Bioinformatics Webinar/Seminar. ECS124 Bioinformatics. Notes on Substitution matrices - PAM and BLOSUM [ Substitution matrices] More Class Notes, Posted 2006 [ Notes on aligning a string to a profile] More Class Notes, Posted 2008 [ Notes from the May 6, 2008 lecture - rant on how to misuse probability] Class Notes for Professor Koehl's LectureMay 15, 2008 [ Koehl May 15, 2008] Notes on aligning three seqeuences, Posted 2008 [ Exact DP for sum of pairs criterion for three sequences. [ Final exam from 2005 ] [ Final exam from 2006 ] Sorry, I don't have any answers to these specific final exam questions.
Lecture Videos: Lecture Videos These are lecture videos taken in 2002. Recommended Papers ECS124 Recommended Papers in Bioinformatics Announcements Announcements (Midterm Solutions, toyblast from lab 6, and other new posts, updated May 20, 2008) Resources General, useful on-line resources. Appendices. Daniel M. Gusfield. Perl for Bioinformatics and Internet. Resources ¦ Computational and Evolutionary Biology (Faculty of Life Sciences – The University of Manchester)
The following list contains links to the on-line resources provided by our research group. Should any of the links be broken or for general enquiries please contact: bioinformatics-webmaster@manchester.ac.uk Please refer to the following web pages for information regarding the Principal investigators and their research interests.
Databases Database search tools Sequence analysis and visualisation software Microarray analysis Network visualisation Structural biology Workflow management Text mining and annotation tools Bioinformatics tutorials. Royal Society. Bioinformatics Tutorials,Bioinformatics Online Tutorials,Bioinformatics Tutorial Guide. Home | Bioinformatics Training Network. Welcome to Rost lab: Overview. Tutorials. Ensembl Login/Register More ▼ Search all species Search Ensembl genomes Search Vega Search EBI Search Sanger Select a species In this section On this page Coursebooks and online documentation Ensembl Tutorials and Worked Examples Online tutorials Introduction to Browsing Chordate Genomes - a 3-hour comprehensive interactive tutorial aimed at beginnersFilmed API workshop - 3 hours of video lectures from an Ensembl API workshop, with exercises to carry out in your own time Video tutorials The tutorials listed below are Flash animations of some of our training presentations.
Note that we are now hosting all our tutorials on YouTube (and 优酷网 for users in China) for ease of maintenance. Coursebooks and online documentation Using the Ensembl genome browser The following examples are available in PDF format: See also our protocols articles on browsing with Ensembl. Printable mini-course Educational resources Genomes and SNPs in Malaria BioMart Data Access with the Ensembl Perl API Permanent link helpdesk@ensembl.org. Bioinformatics.ca.
Pharmbio. Bioinformatics Courses and Lectures. Webinars. NIH VideoCast - Search. General Search Instructions Enter a term in the "Search" box, and then click "Go. " Results appear. To search within the results, make sure the "Search Within These Results" option is selected, enter another search term, and click "Go. " As you search for terms, they become filters and appear in the "Query Refinements Applied" section.
To remove filters click the red "x" next to the term you want to delete. To clear results and query refinements and begin a new search, click the "Search" tab. Filter By Category To sort results by Videocast categories, search for a term then select an option from the "Filter By Category" section such as "Advisory Boards" or "Conferences. " Most Common Terms When you search for a term, related terms and phrases appear in the "Most Common Terms" section. Filter by Date or Change Number of Results per Page Enter a search term in the "Search" box, and then click "Advanced. " University of Illinois Crop Sciences > Matt Hudson Lab > Bioinformatics&Plant Genomics > CPSC 565: Perl and Unix for Bioinformatics. CPSC 565: Perl and Unix for Bioinformatics (syllabus) Perl and UNIX: Lecture 1, introduction to UNIX (powerpoint file) Perl and UNIX: Lecture 2, UNIX for bioinformatics (powerpoint file) Perl and UNIX: Lecture 3, introduction to Perl (powerpoint file) Perl and UNIX: Lecture 4, Perl for Bioinformatics (powerpoint file) Perl and UNIX: Lecture 5, Advanced Perl for Bioinformatics (powerpoint file) Perl and UNIX: Lecture 6, Advanced Perl and Bioperl (powerpoint file) Perl and UNIX: Lecture 7, Advanced Perl and Bioperl (powerpoint file) Cheat sheet for Perl and UNIX (pdf file) Homework assignment (pdf file) Ubuntu Live CD for Intel/AMD 32bit machines (iso file) Ubuntu Live CD for Mac(PPC) (iso file)
Search VideoLectures for Bioinformatics. Welcome to ANGUS! — ANGUS 2.0 documentation. Note These tutorials are checked at the time of posting, but many are now quite old and out of date. The GED Lab does maintain a set of up-to-date tutorials on sequence analysis, the khmer protocols, which may cover similar topics. Major updates and news on future courses (this and others!) Will be posted to the ngs-course-announce mailing list; join to keep up.
This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0). Please feel free to copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. You can find the source code for this material under git version control on github at However, presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation. Bioinformatics Tutorials. August 10th, 2009 by Kristi · 1 Comment There are a number of great tutorials on the web for bioinformatics-related applications and topics. Here are a few that I’ve run across. Are there any missing? Feel free to add any that I might have left out in the ‘comments’ section! BioInformatics Tutorials Series (BITS) from Countway Library of Medicine at Harvard and the Engineering and Science Libraries at MIT by Paul Bain, Courtney Crummett and David Osterbur Research Tips: Molecular & Cellular Biology from Health Sciences Library, Anschutz Medical Campus, University of Colorado Denver Bioinformation FAQs on a TON of topics written by Yannick Pouliot at Lane Medical Library (Stanford) “How Do I?”
OpenHelix Tutorials Additionally, Model Organisms are a key tool for biomedical research, leading to breakthroughs in all fields of biology. National Library of Medicine NCBI Tutorials Other helpful resources from NCBI: EBI Tutorials ShareThis. Microarray Analysis: 2007. Institute for Mathematics and its Applications (IMA) - PROGRMAS/ACTIVITIES. Probability and Statistics in Complex Systems: Genomics, Networks, and Financial Engineering, September 1, 2003 - June 30, 2004 Organizers: Michael A. Newton Department of Statistics and Department of Biostatistics and Medical Informatics University of Wisconsin-Madison newton@stat.wisc.edu and Giovanni Parmigiani The Sidney Kimmel Comprehensive Cancer Center and Department of Biostatistics Johns Hopkins University gp@jhu.edu Technological advances and resources created by genome sequencing projects have enabled biomedical scientists to measure precisely and simultaneously the abundance of thousands of molecular targets in living systems.
Various microarray technologies for measuring RNA transcript abundance have created some challenging statistical problems. Medar - media archive. EDU @ isb-sib.ch. List of free tutorials. What are the best bioinformatics course materials and videos (available online)? Tobias Rausch.