I was at a training workshop in Portugal recently, and whilst there I entered into a rather fruitless conversation about the usefulness of a certain software tool in bioinformatics training. I won’t bore you with the details. I came to the conclusion that there are many different types of trainee, and I wanted to paint a portrait of a certain type of trainee that I have come across fairly frequently, and then see how realistic readers of this blog think that portrait is.
DISCLAIMER: I encounter many trainees, in person and through my blog/twitter feed; they come from many different institutes and universities around the world. The portrait below by no means reflects any specific individual or project, and they certainly do not reflect experiences at any particular institute or institution, including my own.
Inspired by Welch et al, I thought I would create a persona! Here goes:
Ian has just started a 4-year PhD project with Professor Lollipop, an internationally renowned A. bacterium expert. A. bacterium is pathogenic to both humans and animals, and is found in soil and water. Ian’s project involves the sequencing and analysis of 1000 environmental and clinical samples of A. bacterium, including genome assembly, genome annotation, SNP calling, phylogenetic comparison and biological interpretation. The project therefore requires significant bioinformatics expertise. Prof Lollipop does not have any of the bioinformatics skills necessary to do this himself, and nor do any of Ian’s other co-supervisors. Ian graduated from the University of Westeros with a 2:1 in Microbiology, and accepted this PhD project immediately after graduation. Ian’s experience of bioinformatics is a week long course on how to use Galaxy during his second year. Ian has heard of Linux/Unix, but has never worked on that platform. Ian is bright and enthusiastic, and has a good knowledge of how to use Windows and Microsoft Office. The institute where Ian is doing his PhD has some Linux/Unix servers, but Ian needs to demonstrate competence before he will be allowed to use them. The institute offers Linux/Unix training, but this is only run every 6 months and there is a waiting list. The servers themselves use a slightly obscure version of Linux that is 1 major version out-of-date. Ian would not be allowed to have admin rights on these servers and couldn’t install any software. He would be allowed to install software to his home directory, but any software that depends on up-to-date system libraries or software would not work. The institute does not allow Ian to use external clouds such as Amazon EC2 as they consider them unsecure. Ian’s project comes with £5,000 per year to spend on consumables (a total of £20,000) but only £500 from the entire budget has been allocated to training, and that has already been given to the institute to fund their “core skills” training programme – which includes “paper writing”, “how to use powerpoint” etc workshops. Ian has been tasked with learning the skills he needs to do the data analysis himself, and is very keen; however, he is also extremely worried that he may not be able to complete his PhD as he doesn’t have those skills and nor does he feel he has the support to acquire them.
So, question – do you think this is common? Have you come across this type of person? Are you this type of person? Please comment below!
Now let’s extend the imagined scenario above to include the trainer:
Ian has managed to persuade Prof. Lollipop to fund a week long training course on NGS analysis at the University of Middle Earth. You are the tutor on this training course. Ian’s entire PhD depends on your ability to teach him everything he needs to know about bioinformatics. Go!
Are you a trainer who has experienced this? Thoughts? Comments?