Forum:Where To Look For Quality Bioinformatics Short Courses And Workshops?

Question

[Eric Normandeau]

As a source of ongoing training for myself and other members of our lab/institute, I am looking for quality bioinformatic short courses and workshops.

For example, Cold Spring Harbor Laboratory offers workshops on different bioinformatics subjects.

Where do you look for such quality bioinformatics training? Please include links.

Note: by 'short courses', I mean courses that last a maximum of 1 week rather than courses that are taken over a semester, for example.

EDIT: Great answers, keep them coming and give them up-votes if you find them useful!

Even though most of the courses are already passed, some material is still available and sometimes the licences are permissive enough so that you can re-use the material to teach at your local facility/department.

[Malachi Griffith]

This BioStars post seem relevant: Links To Good Next Gen Sequence Analysis Training Courses And Centres

Answer 1

[dwaggott]

These are grrreat!

Canadian Bioinformatics Workshops

• Exploratory Analysis of Biological Data using R (2013)
• Bioinformatics for Cancer Genomics (BiCG) (2013)
• Informatics for RNA-sequence Analysis (2013)
• Informatics on High Throughput Sequencing Data (2013)
• Pathway and Network Analysis of -omics Data (2013)
• Flow Cytometry Data Analysis using R (2013)
• Microarray Data Analysis (2013)
• Informatics and Statistics for Metabolomics (2013)

[Malachi Griffith]

I edited this post to add titles and links for this year's courses to give a better idea of the kinds of things covered. For the last few years, these courses have been held primarily in beautiful downtown Toronto. The courses occupy a single block of time in the summer allowing people who come from other countries the opportunity to take several in a single year without taking multiple trips. I would also note that materials from these workshops are made freely available under a creative commons license.

[jobinv]

I can vouch for these courses; I've learnt a lot by attending them!

[Eric Normandeau]

They indeed look great. Even though there is no scheduled workshop in the near future, I'll skim through the available material.

[rob234king]

The lecture content looks good and by the titles and pdfs I would like to go but is the workshop exploratory discussion or is there a practical walkthrough in the workshops, i.e. like the analysis of a cancer genomics data set vs a control for instance? I would be very interested in the detailed analysis and tutorial of cancer genomic data. Otherwise I can read through the pdfs.

[Malachi Griffith]

Yes, most of these workshops have very hands on and practical walkthroughs. This course covers analysis of cancer genomics data from various angles. This course is focused on RNA-seq but all tutorials and demonstration analyses are based on human tumor/normal comparisons.

Answer 2

[Emily]

We run free Ensembl courses: Free Ensembl Courses

[Eric Normandeau]

VERY nice. Thanks.

Answer 3

[Istvan Albert]

Disclaimer: I serve as a organizer and instructor on the summer course titled Analyzing Next-Generation Sequencing Data (ANGUS) initiated by Titus Brown and held every summer at the Kellogg Biological Station, Michigan State University. This course is substantially reworked and improved from year to year.

• Announcement: Analyzing Next-Generation Sequencing Data, 2014.
• Announcement: Analyzing Next-Generation Sequencing Data, 2013. List of Tutorials for 2013
• Announcement: Analyzing Next-Generation Sequencing Data, 2012. List of Tutorials for 2012
• Announcement: Analyzing Next-Generation Sequencing Data, 2011. List of Tutorials for 2011

Answer 4

[David Langenberger]

NGS Data Analysis Workshops 2023

Also ecSeq Bioinformatics updated their website with their hands-on workshops in 2023:

• May 15-17: Bioinformatics Pipeline Development with Nextflow (Leipzig, Germany)
• September 4-8: 7th Berlin Summer School 2023 (Berlin, Germany)
• October 23-25: Online Course - A Practical Introduction to NGS Data Analysis (Online)
• November 8-10: Single-Cell RNA-Seq Data Analysis: A Practical Introduction (Berlin, Germany)
• November 15-17: Online Course - Bioinformatics Pipeline Development with Nextflow (Online)
• November 29 - December 1: Next-Generation Sequencing Data Analysis: A Practical Introduction (Munich, Germany)

Interested? Apply now

Find a list with all courses here: https://www.ecseq.com/workshops/ngs-data-analysis-courses

Answer 5

[rtliu]

UC Davis Bioinformatics Training Program

"We at the University of California, Davis Bioinformatics Core seek to change that by offering a number of workshops, boot camps, and courses focusing on various aspects of bioinformatics and biostatistics."

"We offer a number of intensive 2-day workshops on RNA-seq, data analysis and visualization, and cloud computing with a focus on Amazon’s computing resources. We also offer a week-long Bioinformatics Short Course, covering in-depth the practical theory and application of cutting-edge next-generation sequencing techniques. Most recently, we’re offering a number of intensive but easy-to-digest 1-day boot camps providing practical answers and hands-on techniques to the hottest topics in bioinformatics. All courses provide ample time for personalized help from workshop professors."

June 2013 courses list:

• June 21, 2013 bootcamp: Cloud Computing for Bioinformatics
• June 20, 2013 bootcamp: Introduction to RNAseq
• June 19, 2013 bootcamp: Introduction to Galaxy
• June 18, 2013 bootcamp: Next-Generation Sequencing Fundamentals

Answer 6

[Thomas Dan Otto]

I am leading and teaching the courses below, so contact me if you need further information.

Glasgow Bioinformatics Workshops 2018 / Bioinformatics Summer School general introduction to Bioinformatics and next-generation sequencing with Linux, R, NGS, mapping, SNP calling, RNA-Seq, single Cell-RNA and ChipSeq. No knowledge is expected and pitched for PhD students and postdocs. 2018 the course will run from the 20-24 of August 2018, application deadline 19/07/2018.

Assembly and Annotation of genomes in Berlin (Physalia Courses), really just focusing on Assembly (75%) and Annotation (25%). Expects basic knowledge of Linux. In the course of 2018, we had a wide range of expertise from people that want to assemble their first genome to experts that wanted to discuss their strategies.

Working with Parasite Databases 2018 in Malaysia, rotates between South America, Africa and South-East Asia. Has 50% on Linux, Genomic and Transcriptomics of NGS, and then links nicely into the EupathDB databases. We will just accept an application from the region.

[Eric Normandeau]

The Assembly and Annotation of Genomes course was great. Thanks again for the knowledge we gained from your course.

Answer 7

[francis]

The 2015 edition of bioinformatics.ca workshops are here

Most in Toronto, but also in Vancouver, Montreal and Halifax (and in NYC in 2 weeks, but those are fully booked this year)

• Introduction to R - May 20, 2015 Downtown Toronto, ON
• Exploratory Analysis of Biological Data using R - May 21 - May 22, 2015 Downtown Toronto, ON
• Bioinformatics for Cancer Genomics - May 25 - May 29, 2015 Downtown Toronto, ON
• Pathway and Network Analysis of -omic Data - June 1 - June 3, 2015 Downtown Toronto, ON
• Microarray Expression Analysis - June 4 - June 5, 2015 Downtown Toronto, ON
• Informatics for RNA-seq Analysis - June 8 - June 9, 2015 Downtown Toronto, ON
• Informatics on High-throughput Sequencing Data - June 10 - June 11, 2015 Downtown Toronto, ON
• Informatics and Statistics for Metabolomics - June 15 - June 16, 2015 Downtown Montreal, QC
• Introduction to R (BC) - June 17, 2015 Vancouver, BC
• Exploratory Analysis of Biological Data using R (BC) June 18 - June 19, 2015 Vancouver, BC
• Analysis of Metagenomic Data (2015) June 24 - June 26, 2015 Halifax, NS

Material from previous years (mixture of PDF/PPT/and video (screencasts) are here.

Answer 8

[Rm]

One of them online at bioinformatics.org: Educational services

[Eric Normandeau]

Has anybody used their services for training? I would like to have your opinion about it.

Answer 9

[Josh Herr]

The Next-Gen Sequence Analysis Workshop (2013 link) -- held in June during the past three years -- is a great course run by Titus Brown, Istvan Albert, and others.

Answer 10

[rob234king]

If in the UK you can sign up to a module(s) from the Cranfield University MSc in Applied bioinformatics which have a taught week and an assignment to complete for the following week.

or

Work independently from tutorials then look for perhaps an advanced course. There is a limit to how much a course can teach you in a week so I think it is advisable if the learner is a biologist with no bioinformatics experience to start with some tutorials first in which they can go at their own pace.

See link: http://elvis.ccc.cranfield.ac.uk/CUBELP2/

[Eric Normandeau]

I agree that there is a limit to what a person can learn in a week, but I am thinking more in terms of continual training and workshops can be great for that. I'll look at the CUBELP tutorials, thanks!

Answer 11

[Giovanni M Dall'Olio]

Leipzig, Germany

• The Programming for Evolutionary Biology is held every year in Leipzig, Germany. It is a 2-3 weeks, workshop aimed at evolutionary biologists wishing to acquire and improve programming and bioinformatics skills. I teach some classes in this workshop. Students learn how to survive in a Linux environment, get hands-on experience in two widely used programming languages (Perl and R), and statistical data analysis. The classes are given by experts in the field and consist of lectures and exercises with the computer. The aim of the course is to provide the students with the necessary background and skills to perform computational analyses with a focus on solving research questions related to genomics and evolution.

Barcelona, Spain

• Next Generation Sequencing for Medical Genomics (Universitat Pompeu Fabra): This course has the aim to familiarize the students with the different NGS technologies and their applications to the study of human genetic variation and disease. The course will cover aspects from technology and informatics to experimental design and data analysis. Course disigned for: master and PhD students preferentially with a background on human genetics.
• Bioinformatic Analysis for Next Generation Sequencing Data (CNAG): This course, which is coordinated by Simon Heath from the National Centre for Genomic Analysis (CNAG), will cover the theory and practical aspects of NGS data analysis, covering different genomic, transcriptomic and epigenomic NGS analyses. The course is disigned for masters and PhD students with an interest in NGS data handling and analysis and will focus on the computational and statistical challenges inherent in NGS data analysis

[A. Domingues]

I can vouch for the course Programming for Evolutionary Biology. Intensive but one does learn a lot, from basic command-line usage to population genomics. It was fantastic.

Answer 12

[Emily]

[EBI holds training on various topics] throughout the year in Cambridge and can deliver roadshows elsewhere. There's also a Train Online platform to learn in your own time.

Answer 13

[carlopecoraro2]

We are running different Workshops in Berlin: https://www.physalia-courses.org/

Best,
Carlo

Answer 14

[radhika]

we would also suggest to take short term bioinformatic trainings/ workshops organized by ArrayGen technologies Private Ltd.

Please visit our link for more details.

http://www.arraygen.com/workshop-training.php

Answer 15

[francis]

Here is what will become a yearly update on this one :)

Our 2021 CBW workshop series: https://bioinformatics.ca/workshops/

1. PNA - CBW’s Pathway and Network Analysis workshop (May10-12, 2021)
2. MLE - CBW’s Machine LEarning workshop (May 25-26, 2021)
3. CAN - CBW’s Cancer ANalysis workshop ** (Jun 7-11, 2021)
4. MET - CBW’s METabolomics analysis workshop (Jun 16-18, 2021)
5. INR - CBW’s INtroduction to R workshop (Jun 21-22, 2021)
6. AUR - CBW’s Analysis Using R workshop (Jun 28-29, 2021)
7. MIC - CBW’s MICrobiome analysis workshop ** (Sep 1-3, 2021)
8. RNA - CBW’s RNA-seq analysis workshop ** (Sep 8-10, 2021)
9. EPI - CBW’s EPIgenomics Analysis workshop ** (Sep 13-15, 2021)
10. ETA - CBW’s Environmental Transcriptomics Analysis workshop (Sep 20-22, 2021)
11. HTG - CBW’s High Throughput Genomics analysis workshop ** (Sep 27-29, 2021)

12. IDE - CBW’s Infectious Disease Epidemiology analysis workshop ** (Oct 4-6. 2021)

    ** Workshops using AWS, and needing some Unix experience (Unix pre-workshop 1/2 day included in registration fee)

[francis]

And this year we are doing a better job at adding YouTube version as the course finishes, a problem with production in the past!

https://www.youtube.com/channel/UCKbkfKk65PZyRCzUwXOJung/featured

(these are free, under CC SA-BY license, like all of the bioinformatics.ca material :)

Answer 16

[francis]

Here is the 2023 update from the Canadian Bioinformatics Workshops (CBW) edition

https://bioinformatics.ca/workshops/current-workshops/

• CBW's Pathway and Network Analysis - June 05-07, 2023 -- Location: Toronto, Ontario, Canada
• CBW's Introduction to R - June 26-27, 2023 -- Location: Toronto, Ontario, Canada
• CBW's Analysis Using R - June 28-29, 2023 -- Location: Toronto, Ontario, Canada
• CBW-IMPACTT Microbiome Analysis - July 05-07, 2023 -- Location: Calgary, Alberta, Canada
• CBW's Metabolomics Analysis - July 06-07, 2023 -- Location: Edmonton, Alberta, Canada
• CBW's RNA-seq Analysis - July 17-19, 2023 -- Location: Toronto, Ontario, Canada
• CBW's Single Cell RNA-seq Analysis - July 20-21, 2023 -- Location: Toronto, Ontario, Canada
• CBW's Machine Learning - August 16-17, 2023 -- Course Mode: Online
• CBW's Epigenomics Analysis - October 11-13, 2023 -- Course Mode: Online

Cheers to all,

francis

Answer 17

[Brian Bushnell]

JGI has a 1-week workshop on primarily microbial and metagenomic analysis a few times per year. The next one is coming up in September 14, 2015.

Answer 18

[Josh Herr]

I'll jump in also and say that I co-teach a Metagenomics short course with Ashley Shade held at Kellogg Biological Station, Michigan State University. This course was formed as a companion to Titus & Istvan's Next Generation Sequencing Course. The course page can be found here: http://edamame-course.org/. We post course tutorials and information here for those not able to attend in person.

Answer 19

[modarzi]

Hi,

In coursera.org you can find Bioinformatics Specialization that is perfect sources for learning bioinformatic. based on below link you can find 7 courses under bioinformatic:

https://www.coursera.org/specializations/bioinformatics#courses

Best Regards,

Mohammad

Answer 20

[Edinburgh Genomics Training]

Edinburgh Genomics offers some great courses on a range of genomic topics http://genomics.ed.ac.uk/services/training

Answer 21

[carlopecoraro2]

You can access the updated course list provided by Physalia-courses in 2023 by clicking here