Data integration in microbial genomics ... - Jacobs University
Data integration in microbial genomics ... - Jacobs University
Data integration in microbial genomics ... - Jacobs University
Create successful ePaper yourself
Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.
88 7. Summary and discussion<br />
for a given sample over time along the workflow presented <strong>in</strong> Figure<br />
1.7 and to keep track of samples.<br />
MetaBar received considerable attention after it was published. The<br />
BioMed Central Editorial board <strong>in</strong>formed the authors per email, that<br />
the article was accessed 2688 times 1 <strong>in</strong> the first four months after publication.<br />
The paper earned the attribute ’highly accessed’. Despite of<br />
this fact and even though the tool was successfully applied <strong>in</strong> several<br />
use cases such as the yearly repeat<strong>in</strong>g <strong>in</strong>troductory week of the Mar<strong>in</strong>e<br />
Microbiology (MarMic) Master class on Sylt, <strong>in</strong> general it has to be<br />
stated that the tool has not yet created a wider impact <strong>in</strong> the life science<br />
community that is reflected <strong>in</strong> a large user community.<br />
This can have several reasons. Of course, this additional ’bookkeep<strong>in</strong>g’<br />
puts an extra burden to biologists. It can also be that MetaBar<br />
will be used more, when the usage of the MIxS standards is promoted<br />
more widely. Due to the implementation of a user management with<br />
SSL encrypted user authentication, local <strong>in</strong>stallations became complicated.<br />
User accounts for the MetaBar <strong>in</strong>stallation hosted at the MPI<br />
Bremen are given to <strong>in</strong>terested users outside the <strong>in</strong>stitute. But this<br />
service has not significantly been requested. Though it has been tried<br />
to implement a straightforward workflow, the <strong><strong>in</strong>tegration</strong> of various<br />
features (e.g. permission concept, exports and submission to INSDC)<br />
<strong>in</strong>to MetaBar resulted <strong>in</strong> a complexity of the tool, that possibly scares<br />
off potential users. Though detailed documentation how to use the tool<br />
is available, experience collected at the MarMic <strong>in</strong>troductory courses<br />
on Sylt, showed that an expert needs a couple of days to teach novices<br />
<strong>in</strong> the usage of MetaBar. Though the contextual data that is captured<br />
with MetaBar can be prepared for submission to the INSDC, this was<br />
not the primary focus of the tool and the <strong><strong>in</strong>tegration</strong> of this feature<br />
has been done towards the end of the MetaBar development phase.<br />
These observations motivated the development of the follow-up tool<br />
CD<strong>in</strong>Fusion, with a clear focus on sequence and contextual data submission<br />
to the INSDC. It was aimed to avoid many of the negative<br />
effects described above, which potentially hamper the impact of such<br />
a tool. S<strong>in</strong>ce it is required by journals that biologist who analyze sequence<br />
data <strong>in</strong> publications have to submit their data to INSDC, it<br />
puts no extra burden to the biologists to prepare these submissions.<br />
1 This number is not <strong>in</strong>clud<strong>in</strong>g access from PubMed Central or other archive sites.