IBERS, 11 December 2014
Bioinformatics Training Coordination
Attendees:
Tanya Dickie, TGAC
Narcis Fernandez, IBERS
Chris Creevey, IBERS
MAIN QUESTIONS
What training already exists, i.e. training programme for 2015?
Only the basics, e.g. Linux, HPC for postgrads – more reactive, ad hoc training
provided 1:1, or send people externally
Regular seminars and workshops are run on more technical topics – supply and
demand dictates which topics are covered, e.g. RNA Seq, different aspects of
covered in different workshops. Usually just an hour, but enables people to get an
overview and potentially ask the right questions.
Ensembl roadshow has been run in the past, with someone external coming in to run
the course.
Computer science dept runs Python courses which are open to people from IBERS –
been successful.
There is no training budget, part of Bioinformatics researchers’ remit is to do
training, but not clearly articulated – not really well structured. New position to be
recruited is the only resource devoted to training. There is a training budget
element but more personal development.
Department is trying to centralise provision of resources for Bioinformatics
researchers, cloud computing facilities for VMs, dedicated storage for sequencing
data, plus various other resources including FTEs such as a dedicated Bioinformatics
assistant who works with students and their data.
Only 4 people to run infrastructure for a huge facility.
Other comments
Difficult to ensure all relevant training is provided, especially when there are so
many disciplines in one place, e.g. proteomics, metabolomics, phenomics.
They do send people to external courses as training not in place currently at IBERS.
Concentrate on providing a couple of core things and do them well, but difficult to
do so with such a wide variety of research roles.
IBERS, 11 December 2014
Bioinformatics Training Coordination
Ability to harness training courses/facilities in rest of university.
IBERS don’t have a training department – once two smaller institutes merged, didn’t
have infrastructure to support larger institute.
New Director has been appointed recently so hopefully progress will be made in
various areas. Large investments in technology, e.g. sequencing centre, plus
significant investment from Welsh govt to innovation campus to enable small
companies to come in and work with various departments, e.g. proteomics. Massive
automated plant phenomics centre.
Not had the resources to write training up to this point, other than basics such as
Linux, plus webcasts in using Galaxy platforms.
New recruit will have a lot of work to do to tap into expertise in various departments
by converting into training materials, whilst also checking to make sure training isn’t
already available on platform/can be adapted from materials on platform.
They are a university department so provide undergrad as well as postgrad training.
Most of the masters/undergrad courses are in biology, not bioinformatics – distance
learning has recently been rolled out in masters for rumen microbiology.
Who is involved at Institute?
Narcis. Chris, Martin Swain (senior lecturer in NGS) plus 4 different Bioinformatics
core facilitators – some faculty involved in a functional genomics course for 3rd year
undergrads, plus some masters courses
Other comments
A lot of resources in biological sciences as part of the university.
A lot of contact with relevant industries – cofunding on research projects, working
together towards goals, research in a commercial setting
Will be up to individual institutes to decide what is appropriate to upload to
platform, TGAC will not police the platform
IBERS has expertise in house which can be translated into training, where there is a
gap/need
What would you like to see developed?
Email was sent out to IBERS to ask for their feedback.
IBERS, 11 December 2014
Bioinformatics Training Coordination
Use large investment facilities for specific training to use expertise in specific
processes, with new recruit who should know how to write training, with the help of
researchers.
Take some of the highly in demand expertise and implement, such as Galaxy training
How do I define best practice when everything changes all the time, treat things like
Galaxy as a black box and don’t consider the parameters changing – giving people
the confidence to change processes to adapt them to their own needs.
Experiments need to be designed so they can be analysed bioinformatically
afterwards – experimental design.
Implementation of pipelines in Galaxy – Galaxy is highly desirable from a
researcher’s perspective as it’s easy to use, but from a technical/admin point of view
it’s very difficult to maintain as data difficult to store and privacy issues.
Other comments
See printout
IBERS, 11 December 2014
Bioinformatics Training Coordination
QUESTIONS FROM IBERS
Development of our own computational tools/software – use github for distribution,
but all very disparate – like to try and translate that into something that’s useful for
the wider community – is there a role for that in this online platform?
Yes definitely – won’t be used for storing source code, github will still be used for
that.
Will there be a central resource to help turn software into a training course?
Not so much guidelines to write training, expectation will be that training
coordinators will already have experience in doing that and will be in job
descriptions/intrinsic part of recruitment process.
There should be guidelines as to how to write training so that new recruits are given
guidance as to how to convert software e.g. into training materials – otherwise it
may end up as a cacophonous mixture of disparate/incompatible training materials
that are difficult to navigate around.
Fair point, need to check and come back to them
Is there a common platform to share tools, e.g. Galaxy, so that people could provide
plug in tools so that their tools can be used?
Good point, need to check and come back to them – meeting in February will
hopefully ascertain but I will speak to Andy Law about his software best practices
meeting to see that someone from IBERS has been invited
Will there be any formal meetings of the coordinators going forward?
Yes there will be regular catch ups, not f2f but go-to meetings/Skypes etc and as
there is travel in the budget, there will be the option to visit other institutes as
necessary/appropriate.
Will there be a discussion forum for the training materials, rather than using free
text - community forum for specific queries? What if we’re asked a question we
can’t answer, how do we farm out questions to people who can answer the
questions – accessibility of training will enable people to ask more questions?
Not sure, maybe collaborative blog can be slightly used for that but a good question,
need to check and come back on that.
Will trainers be responsible for answering all questions on their topic?? Maybe use
“SeqAnswers”, embed it within Drupal platform – rather than loading lots of
questions onto one person.
Good point, need to speak to Drupal consultant to ask about the feasibility of
embedding it within platform.
How will it be decided which version of maybe basic training will be used across the
institutes?
Hopefully it will be obvious which versions are best and institutes will be happy to
used the best version, rather than insisting on using their own.
IBERS, 11 December 2014
Bioinformatics Training Coordination
How will sharing of information be organised effectively, to avoid waste of
time/duplication of efforts?
February meeting will be used to make the decision by all the institutes, but my
report will provide guidance and the meeting will have a strict agenda and I will be
chairing it.
Quality control will be an issue?
There will be an informal peer review process in place, via use of ratings system and
feedback – have a report as abuse style button!!!!
Long-term sustainability of project – not much point putting all this work in if it
won’t be continued.
Can’t answer that, dependent on BBSRC funding.
Will TGAC’s training suite be open to hosting other institutes’ courses, e.g. IBERS
courses at TGAC?
Not sure if we would be able to host other institutes’ courses, but a collaborative
effort would definitely be encouraged, e.g. IBERS trainer plus TGAC/IBERS attendees.
IBERS, 11 December 2014
Bioinformatics Training Coordination
MISCELLANEOUS
Current Training Facilities?
Large bioinformatics hub, drop in space for hot desk computing and potentially
training – space for biologists to come and sit down and work with bioinformaticians
to help them manipulate their data.
Some reorganisation of space is needed.
Training facilities at university can be used out of term time – maybe something that
the new coordinator can look into using long term but also lobbying for funds for
events management people.
How do you think this online platform will help?
Providing a central resource for researchers in the department to go to will provide a
first response to a need – very valuable. Information needs to be well-organised and
documented so resources are easy to find – the contactability of the people involved
will be invaluable, e.g. being able to email trainers with questions.
Different institutes are more possessive of their own areas, so if this helps to open
up communications and shareability amongst institutes, it will be a good thing.
Will be open access to everyone rather than just institutes, will be a good thing.
IBERS, 11 December 2014
Bioinformatics Training Coordination
What is the grant money being used for?
Currently in process of being recruited – with HR, job description still to be
translated into Welsh!
Job description has been floating around since July, but has been held up by
authorisation process and various bureaucracy – need to chase again but not
hopeful it will be advertised by the end of the year. Processes are bureaucratic and
lacking in communication – an art writing a job description for universities!
IBERS, 11 December 2014
Bioinformatics Training Coordination
CONCLUSIONS / SUGGESTIONS
Include a chat forum to enable discussions around training etc – integrate with blog.
Draw up best practice guidelines around writing training courses – sharing of
expertise at February meeting to start drawing them up and build on them.