Roslin, 23 January 2015
Bioinformatics Training Coordination
Attendees:
Tanya Dickie, TGAC
Andy Law, Roslin
MAIN QUESTIONS
What training already exists, i.e. training programme for 2015?
MSc course in bioinformatics for potential PhD students, within research groups,
people already have training in Bioinformatics and Biomathematics so there is no
major need for training in application, but there may be a need for training in the
skills to develop the applications…more relevant to the software engineering project.
Some basic training courses, twice a year – also access to University training
programme, plus access to University super computer (“Eddie”), access to “Archer”
UK super-computer – in next year or so, will have on generalised access to super
computing and then designing training for Roslin will become so much easier as will
be only one path to the training. Only specific to Roslin’s infrastructure though.
Basic induction courses, including writing scientific notebook entries electronically vs
using paper. Use RT rather than Jira. Ensures that all notes are kept correctly,
whichever format is used – may not be Bioinformatics courses, but important to
record.
Training is done in-group, via osmosis or you go to another group who can train you
or as last resort, you go externally – healthy funding stream to send post-docs to
external training courses, but not used so much for Bioinformatics/Biomathematics
as not as practical.
Ensembl people do “geek for a week”, but only visiting scheme available at Roslin.
Similar situation in Bioinformaticians being pestered with questions from wet lab
scientists, but it is managed by speaking to Group Leaders, Andy Law facilitating
those conversations by speaking to various people around the institute. Also use
University of Edinburgh for sequencing etc which the groups will be charged for and
the groups will have people in place who know how to manipulate data.
Edinburgh Genomics will do sequencing, will be very distinct from Roslin Research
Institute so line will be drawn internally which will enable computing services to be
defined much more clearly. Will have separate disk space so data relating to
sequencing will be separate from research data.
Other comments
Roslin, 23 January 2015
Bioinformatics Training Coordination
Needs to be means by which to track training records and what training has been
done by whom – e.g. LANTRA at Pirbright, only paper records at Roslin and as with
other institutes, needs to be record keeping to ensure all training is captured.
Difficult to promote generic training, each institute will have slightly different
contexts, so there will be lots of training on the same topic on the platform that look
the same but are slightly different.
Series of lectures to be written and run in various forms of statistics for post-grad
students.
Data management courses, QC lab notebook type application to electronic analyses
– how to track the data you’ve used in your experiment, how to lay out the data in
your notebook – generic course which could be used by other institutes.
Who is involved at Institute?
Largely done in-group so no real team dedicated to training – experts in field in
Roslin will pass knowledge on to their group, as opposed to individuals dedicated to
training.
Other comments
Groups contribute to other groups to provide specific training where that group is
lacking – also able to capitalise on University of Edinburgh Bioinformatics resources.
What would you like to see developed?
Need to teach people generic skills, as well as NGS skills plus genetic analysis
programmes.
Other comments
Roslin, 23 January 2015
Bioinformatics Training Coordination
QUESTIONS FROM ROSLIN
Need to make virtual machines available to access certain training courses, e.g.
LINUX training at Roslin – just by accessing the course, they have access to a Virtual
Machine and datasets – will these be made available via the platform?
Roslin, 23 January 2015
Bioinformatics Training Coordination
MISCELLANEOUS
Current Training Facilities?
How do you think this online platform will help?
Useful exercise across the institutes – merits in not reinventing wheel, tapping into
GOBLET and improving upon it. Other institutes will develop materials we may not
have access to already, but there is a need for so will be good to have relevant
materials available. Will free up time for training if materials are available, won’t
need to be there in person.
Need to ensure that people accessing the platform know whether they need major
computing power in order to run certain courses.
Roslin may not contribute much but will enable their people to access materials they
may not be able to access internally.
Interested in collaborating with IBERS on proteomics etc etc
Giving people the training to be better Bioinformaticians
What is the grant money being used for?
Roslin, 23 January 2015
Bioinformatics Training Coordination
Post to develop training materials – huge range of Bioinformatics already being
focused on in Roslin, so impossible to hire someone who is a specialist in everything,
hire someone who knows about training course development, rather than a
bioinformatician. Hired someone who has developed eLearning materials and has
background in video production – making things effective through presentation.
Started in early January.
Roslin, 23 January 2015
Bioinformatics Training Coordination
CONCLUSIONS / SUGGESTIONS
Needs to be long term sustainability for this project, otherwise materials will
stagnate as post will not be reabsorbed and they will become obsolete rapidly.
BBSRC should core fund this project if bioinformatics training has been identified as
essential to the future of Bioinformatics and Bioinformatics
TGAC may offer sequencing training vs Edinburgh Genomics who will charge for that
– major conflict of interests TGAC vs Art Genomics (Edinburgh Genomics)
Apple.zhang@ - EXTEND INVITE TO HER FOR MEETING IN FEBRUARY
Unimpressed by interface and content of GOBLET portal – ugly list and telephone
directory
elearning interface on University of Edinburgh is pretty good.
Comparagrid – ask Rob Davey