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• Why we’re having this discussion • Reminder of first survey results
• Review of second survey
• Feedback from participants of SEB-GOBLET workshop
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• This workshop will have tangible outcomes • Outputs of this session
– outline of a paper on the state of the field globally • output required for grant funding
– action plan for addressing global & regional needs identified as urgent
• Hopefully, this session will fuel discussion & help to add flesh to those outputs
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• Anecdotal evidence suggested bioinformatics skills shortages/gaps are prevalent amongst life scientists
• Early 2013, conducted a survey of training needs (mostly) within SEB community to get a snap-shot
• Survey deliberately simple • 10 questions using Survey Monkey
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• The aim – for those using bioinformatics tools, to determine the areas in
which they’d like training – level of confidence using bioinformatics tools & resources
– how any bioinformatics E&T had been received
– how people wanted to receive bioinformatics E&T in future – what skills would be particularly useful
• Disclaimer – we are not ‘survey researchers’, so claim no rigour in the process
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• The questions 1. What is your job title? 2. What is your research discipline? 3. In which institute are you based? 4. In which country are you based? 5. What bioinformatics tools/databases/etc. do you use & for what
purpose? 6. How confident are you in using them? 7. How have you acquired your bioinformatics skills? 8. Which bioinformatics skills training would you most value? 9. How would you prefer training to be delivered to you? 10. Any other comments
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• Survey emailed to members of SEB, 1st week Feb 2013 – plus the Biochemical Society & Society of Biology’s newsletters – also ISB, SIB, EMBnet communities…
• & tweeted by TGAC, BBSRC… – results collated 1st week March 2013, from ~210 responses
Observation Countries 75% Europe Respondents/career stage 35% PD/RA, 32% MSc/PhD Respondents/discipline 33% plant science Current learning method 76% self taught/colleagues Level of confidence 33% level 3 (scale of 1-5) Training required 67% analysis/interpretation Preferred delivery method 74% workshop/57% e-learn
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• Survey on training needs amongst Life Scientists
– “Although I am aware of bioinformatics courses, there is not enough publicity or not enough of them to cover our needs.”
– “There should be more awareness that older biologists are very keen to learn new bioinformatics techniques.”
– “It would be great to provide slides from courses.” – “Bioinformatic training is imperative - it should be taught in LS
disciplines at the university. I highly support your initiative.” – “There are so many bioinformatics techniques, softwares, etc, it
would be great to have a central wiki devoted to introducing people to packages & analysis methods.”
– “Large data statistical analysis skills & software are lacking. Need to train more people on this.”
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• Survey on training needs amongst Life Scientists
– “Perhaps a common repository of code for analysis to improve access, use & standards in analysis.”
– “Interpretation is more important than the analysis.” – “I think this is a really good initiative & hope to hear more from it” – “More training in this area is vital for plant scientists to develop their
employability.” – “There are several initiatives out there. Would be great to compile
resources in one place.” – “I think what you are doing is of great value!” – “We need an accreditation mechanism similar to board certification
for MDs & the Bar for lawyers.” – “This is an enormously important questionnaire. Thank you.”
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• 1st survey, simple but informative – even if not rigorous…
• Interest generated during 2013 AGM at TGAC – other GOBLET members agreed to run the ‘same’ survey in their
countries/communities • BioSharing, APBioNet, TGAC, ABN, FEM, Nowgen, NBIC, SGBC,
bioinformatics.ca…
– the aim, to extend the reach of 1st survey, to see how common its findings were amongst global communities of life scientists
– proposed to collate results & write ‘state of the field’ white paper
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• The questions remained the same, but the form of the questions was ‘tweaked’ to make them easier to answer…
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• Circulated to – ABN, who also posted across several channels – ASBCB, who also posted to H3ABionet – SeqAhead, who also mailed to 800 members of the LinkedIn community – Nowgen/UoManchester, who also posted to the Association for Clinical
Genetic Scientists & British Society for Genetics Medicine – ISCB – APBioNet – bioinformatics.ca – SolBio – EMBL – NBIC – IGC – CGAT – Biosharing – SIB, ISB, EMBnet again plus EMBnet.digest announcement – TGAC…
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• Ran for ~18 weeks – ~1st week in February to ~1st week in June 2014
• Don’t know size of full population surveyed – but 498 respondents
• so more than twice the number cf. the first – but it ran for more than 4 times as long!
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• Offer from Sarah Blackford to host an E&T workshop during SEB 2014 AGM – in Manchester, 30June/4 July 2014 – to discuss the findings with a group of life scientists & discern
whether the results of both surveys resonated with them • what are the perceived bioinformatics training needs?
• what are the best options for meeting those needs?
• are UG & taught Masters programmes delivering?
• what should be on the bioinformatics curriculum?
• how can or what can GOBLET do to help?
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Comparison of respondents by job title
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20
40
60
80
100
120
140
SEB GOBLET
Num
ber o
f Respo
nden
ts
Academic/PI
Postdoc/research staff
MSc/PhD students
Technical staff
Other
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SEB respondents by discipline
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Plant science
Biomedical
Microbiology/virology
Marine/fish
Others
GOBLET respondents by discipline
16
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How have you received this training/education?
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100
200
300
400
500
600
SEB GOBLET Summary
No. Respo
nses
Self taught & colleagues
Masters/UG courses/doctoral
Professional training courses/university courses
Internet/online courses
Other
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How would you like to receive this training/education in future?
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Other
Undergraduate programmes at my university
Graduate level programmes at my university
During scienOfic conferences
Summer schools
Courses at place of work
Stand-‐alone workshops
Online/e-‐learning
No. of Responses
GOBLET
18
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Confidence using data-analysis techniques
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Confidence using command-line software tools
20
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Which skills do you require?
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50
100
150
200
250
300
350
400
SEB GOBLET
No. Respo
nses
Analysing & interpreOng data/stats
Programming
Database selecOon and usage
SoVware tools (using correctly + adapOng)
Sequencing analysis
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Online courses are ok if include a good opportunity
to discuss with teachers
Additional comments
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Need user-friendly courses for biologists with no programming
skills
There are so many learning sites/tutorials/tools – it’s difficult to
pick the "best one"
It’s too late for me, we need to fix the undergraduate syllabus - all
biology students should be encouraged to learn programming
and statistics
For beginners, it’s hard even trying to use command-line tools –
courses too advanced for those who’ve never used Linux. It’d help to work through example data in
small groups with a tutor
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• Do the survey results resonate with you? – if not, why not?
• Are there gaps in the results? – if so, what are they?
• What could/should Universities/other providers do to help? – e.g., CPD. If so, in what form (distance, blended, short workshops)?
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• Biologists shouldn't be expected to be skilled bioinformaticians! – they should be able to consult with experts when needed
– we should be reaching out to UGs & really instilling core skills there!
• Help is needed with the analysis & interpretation of data generated by certain technologies & tools
• Standalone workshops & e-learning resources are the preferred routes for acquiring training – universities should provide access to specific software/databases, &
provide training in their use – new users should be given more encouragement & be nurtured more
with some of these tools 16/11/2014 24
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• To instil confidence with bioinformatics tools (& indicate the level of skills acquired during courses), short tests could be provided, perhaps using sample data-sets to test proficiency
• It would help if GOBLET provided discipline-specific examples or case-studies – to illustrate the use of different tools
– to better spark interest & resonate with novice users – the portal could also usefully hold training data-sets to allow users to
gain more confidence in their use
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• Some participants felt that maths/stats were more important to learn than programming – many had no stats/bioinformatics support, so had to find their own
solutions – often via YouTube! • “Google is our best friend!”
• Peer support across different disciplines, & a forum to sound-check tools & seek advice would be valuable – recognised it would require champions to drive this
• The portal could also provide relevant links to Coursera &/or highlight what GOBLET offers that's different
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• In terms of what GOBLET could do to help, it was recommended that – materials provided by the portal should be open source – there should be a mechanism (a rating system?) for discerning the
quality of various materials & tools
• Participants wanted to – see flexible modules held in a searchable portal, which would also
provide the means to share scripts – be able to find points of contact for certain specialist areas – see greater levels of outreach at conferences – learn more about the range of jobs that bioinformatics encompasses
• e.g., during careers days
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• Feedback also suggested that GOBLET could provide guidance/advice on – computing infrastructures – potential uses of the Cloud
• Finally, there was consensus on the need for accreditation of training resources & courses
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• Has anyone done other independent surveys & found additional regional needs?
• What further needs exist in our different geographical regions that may not have been captured in the surveys?
• How can GOBLET address these needs collectively &/or individually at the local level
• What can GOBLET do to address common global needs & common regional needs?
• What resources would GOBET have to put in place?
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