Category Archives: Training

Winter School on Whole Genome Sequence Assembly and Annotation, Switzerland

Message from Stuart Dennis:

Registration is now open for our Winter School on Whole Genome Sequence Assembly and Annotation at Monte Veritá, Switzerland from 4-9 February 2018. Please share this advertisement with your colleagues and students.
The Winter School is a intensive 5-day workshop on how to Assemble and Annotate Whole Sequence Data – with a focus on de novo whole genome assembly and analysis of complex Eukaryote genomes. The Winter School will combine lectures with computer based practicals and will be most valuable to those who have, or will soon have, whole genome sequence data.
Outline of Topics and Instructors
Whole Genome Sequence Assembly John Davey University of York, UK.
Hi-C and 3D Whole Genome Assembly  Olga Dudchenko Baylor College of Medicine, USA.
Whole Genome Sequence Annotation Carson Holt University of Utah, USA.
Manual Gene Annotation Monica Monuz-Torres Phoenix Bioinformatics, USA.
Transposable Element Annotation  Anne Roulin University of Zurich,  Switzerland.
Whole Genome Sequence Annotation Robert Waterhouse University of Lausanne, Switzerland.
Registration closes 10th November 2017
Spaces are limited to 30 participants. See our webpage for more details on how to register
For further enquires please email Jessica Stapley at

Stuart Dennis

Department of Aquatic Ecology


Überlandstrasse 133

P.O. Box 611

8600 Dübendorf


Course UEA Systematic Review and Meta-analysis for Environmental Sciences

11th – 15th September

Systematic Review and Meta-analysis for Environmental Sciences

The University of East Anglia is offering a NERC Advanced Training Short Course on systematic review and meta-analysis for the environmental sciences.

This 5-day course seeks to promote and facilitate the thoughtful and critical use of systematic reviews and meta-analysis for research synthesis in environmental sciences. The course will involve combination of lectures and practical sessions where participants will practice conducting meta-analysis using worked examples in meta for package in R. In addition, participants will conduct their own mini-meta-analyses by working in small groups on an assigned environmental topic and present their results to the class.

Message from Jarek Bryk (U of Huddersfield)

Dear Colleagues,

I am writing to let you know about a new funding opportunity you may not otherwise hear about. Polish National Science Centre has announced a “Polonez” funding for researchers who want to spend up to two years doing basic science research in Poland (open to all disciplines). The financial conditions are quite favourable (4350 Euro gross monthly salary with full employment, plus extras for family allowance) and research grants for up to 160000 PLN (~30000 GBP, ~40000 Euro) for two years for a life science project. The starting date is September 2016, and the deadline for applications is December 15th.

The call and more details are here: and you can email me ( if you’re looking for a project and/or need some help or advice in selecting or contacting a potential host institution in Poland.

Message from Haris, new MOOC on ‘Monitoring Climate from Space’,

Message from Haris:

ESA’s new MOOC on ‘Monitoring Climate from Space, designed and produced by Imperative Space, is now open for enrolment and will commence on 8th June 2015. Thousands of learners have already signed up for the course, and we would be delighted if you would also like to participate, or encourage others to do so.

MOOCs (‘Massive Open Online Course’) are a fast growing form of free online education and training, used by many leading universities and institutions to open up high quality academic courses, professional training and informal learning to new audiences.
This course is ESA’s first foray into MOOCs, and will consist of 30 videos, interactive exercises, online discussions and links to additional resources and optional in-depth reading. It will focus on the role of satellite Earth Observation (EO) technology in monitoring changes in the Earth’s climate and environment, and how satellite data can support climate-related decision making, policy and communication, in areas such as climate-change mitigation, adaptation and sustainable development.
The course features on-screen contributions from leading experts in EO data and climate science, and a wide range of visually compelling EO data and imagery. It will be hosted by FutureLearn, the UK’s leading MOOC platform, which has a heritage rooted in the Open University. The course is free and will run over 5 weeks, with around 2-3 hours of learning time each week.
The enrolment page, with further information and a trailer video, can be found here.
Further details and the ESA/FutureLearn press release can be found on the Imperative Space website here.
And if you would like to share or host the trailer video, you can download this from here.
Discussions about the course on social media will use the hashtag #FLclimatefromspace


Dr. Charilaos Pylidis

Workshop: NGS data analysis, January 7-9

Where : Univeristy of Leicester, UK

What: Next Generation Sequencing Data analysis.

When: 7th-9th January 2015

A few places are still remaining and are available for external applicants. Places will be allocated on a first-come-first-served basis.

Next Generation Sequencing methods are becoming ubiquitous in all areas of biology. This three day workshop aims to enable wet-lab biologists to understand and implement basic pipelines for analysis of NGS data. Topics covered will include:

*         An overview of NGS technology

*         A brief introduction to library preparation

*         Common file formats

*         Quality Control

*         Genome Assembly

*         Mapping

*         Variant Calling

The workshop will consist of a mixture of short talks and practical work. Participants are required to have some basic knowledge of Unix to enable them to follow the practical work.

Further details and the registration form are available on the University of Leicester Bioinformatics and Biostatistics Analysis Support Hub ( Please email me directly if you have any queries.

Kate Lee

Research assistant

Bioinformatics and Biostatistics Analysis Support Hub (BBASH)

University of Leicester

Tel: 0116 252 3350


Workshop in Marine Ecology, Evolution, and Genomics

Hello All,

Just a note that there is a workshop in Vigo this fall, organized in part by APS alumni (and friend) Juan Galindo. Although it is focused on marine organisms, the topics tackled should apply well across organisms (particularly the data handling and analyses bits). Victor will be running a hands-on tutorial as part of the workshop. More info can be found here:

cheers, Patrik

NGS Workshop at Sheffield University Next Week 16th July

Next Generation Sequencing Workshop next week (16th July) at the University of Sheffield (Inox Dine).

Details at this website:

This is a one day course that will give you everything you need from the basic overview to more detailed applications like Exome, Genome and RNA (Transcriptome) sequencing.

There will also be a lab tour of the NGS Facility at the Children’s Hospital to show you the different NGS platforms.

This is a low cost workshop and as part of a collaboration we have with the University we can offer you a 30% discount (off the standard cost of £100) if you book before the end of this week.

In this case use Discount Code 0b69944b when booking online at the above site or call Ed Quazi if you want to book using another system (0161 870 6056). <>

Mentoring for Postdocs

Research career decisions and difficult choices – what’s the point of a mentor?

Are you interested in finding out how having an independent mentor can help you progress in your career, make important choices, and navigate your path? Would you like to know how working with a mentor can help you find solutions for working with a difficult person? Would you like to find out more about how you can use time with your mentor to find balance your work and life?

A brief informal intro session on the post-doc mentoring programme will take place at 2pm on Weds 5th Feb in the Hicks Building (Room F28) Kay Guccione (the programme designer) will be there to show you how mentoring works and how it’s different from (and complementary to) a line-management or supervision relationship. There will also be past participants attending to share their experiences of having a mentor, and help answer any questions you have about the point of mentoring, the way it works, and the benefits for researcher careers.

The mentoring programme is not just for those who are set on an academic career. Making career decisions is a key part of what mentoring can support you with. Mentors focus on helping you to manage your career, consider your options and improve your skills.

Event facilitator: Dr Kay Guccione (Researcher Mentoring and Coaching Manager)

If you have questions and want to know more about the researcher mentoring programme, please contact Kay Guccione (

Course on molecular and computational tools to study the composition and diversity of microbial communities, Liverpool

The Centre for Genome Research is pleased to announce a 2-day course designed to showcase some of the molecular and computational tools that can be used to study the composition and diversity of microbial communities.  The course is being run on Thursday, 28th & Friday, 29th November 2013 in Liverpool and the application deadline is 8.00 a.m. on Friday, 8th November.  You can find further details and the application process via the Centre for Genomic Research website Please note that places are limited but all applications received before the deadline will be treated equally.

The Centre is also supporting the 4th part of the “Balti and Bioinformatics” series being led by Dr. Nick Loman, Birmingham, which comes to Liverpool as “Beatles & Bioinformatics” on Wednesday, 27th November 2013.  Again, the agenda and the registration process can be found via the CGR website.

Please do feel free to contact me if you need any other information about either event.

Best wishes,

Lesley Parsons, Centre for Genomic Research, University of Liverpool

Tel: 0151 795 4509;

Biodiversity training workshops – 26-27/11/13, Cardiff + 5-6/12/13 Manchester

BioVeL, a virtual laboratory for biodiversity research data, is offering two training workshops

  1. Introduction to workflows for taxonomic refinement, biogeographic analysis, and species distribution modelling,November 26-27, 2013, Cardiff University.
  2. Building workflows with Taverna workbench, December 5-6, 2013, Manchester.

Note that these training workshops are free to attend but registration is required. The number of participants is limited.  For further information,
please write

More information on BioVeL: