Biomedical Engineering Reference
In-Depth Information
especially for small tasks. To help with usability we have installed a local
Galaxy [22] instance, this workfl ow engineering and tool integration
environment has been described as the 'missing interface' for
bioinformatics and it is well designed. Biologists can get up and running
command-line tools through Galaxy in no time at all.
11.7 Helping biologists to stick to the rules
In our experience, bioinformaticians can be somewhat recalcitrant when
it comes to telling the biologist that they must format data in a certain
way or follow certain naming conventions. Perhaps this is because they
feel that there will be resistance and that the biologists will not appreciate
this intrusion into their work. Biologists work according to similar sorts
of rules all the time and are quite fl exible in their acceptance of these. For
example, when carrying out their bench experiments, the molecular
biologist will often need to create a piece of DNA that comes from some
organism of interest and fuse it to DNA control sequences that perhaps
come from a different organism, a chimaeric piece of DNA. To use this it
may need to be inserted and activated in a third organism, often bacteria,
creating a genetically modifi ed organism with DNA from two donors. It
is not too hard to imagine that this procedure requires lots of rules,
standard procedures and paperwork so biologists are primed to jump
through hoops when getting things done. When we introduced our new
rules for data and meta-data standards, we did not believe that we would
get much resistance from the biologists, although we were prepared for
quite a lot. We armed ourselves with arguments as to what savings we
would make in time and convenience and future protection against
confusion and data loss and we took these arguments straight to the
group leaders. Convincing the project leaders gave us some authority and
offi cial backing and made it much easier to get the rules adhered to. We
get good uptake of our rules and standards, biologists quickly come to
appreciate the reasons why and after a little while (usually after having to
deal with someone else's fi les) are glad that they have been implemented.
11.8 Running programs
With the environment setup the new user can log on and start to do their
analyses. We use a Debian-based [23] compute cluster to which users
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