Data integration in microbial genomics ... - Jacobs University

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88 7. Summary and discussion for a given sample over time along the workflow presented in Figure 1.7 and to keep track of samples. MetaBar received considerable attention after it was published. The BioMed Central Editorial board informed the authors per email, that the article was accessed 2688 times 1 in the first four months after publication. The paper earned the attribute ’highly accessed’. Despite of this fact and even though the tool was successfully applied in several use cases such as the yearly repeating introductory week of the Marine Microbiology (MarMic) Master class on Sylt, in general it has to be stated that the tool has not yet created a wider impact in the life science community that is reflected in a large user community. This can have several reasons. Of course, this additional ’bookkeeping’ puts an extra burden to biologists. It can also be that MetaBar will be used more, when the usage of the MIxS standards is promoted more widely. Due to the implementation of a user management with SSL encrypted user authentication, local installations became complicated. User accounts for the MetaBar installation hosted at the MPI Bremen are given to interested users outside the institute. But this service has not significantly been requested. Though it has been tried to implement a straightforward workflow, the integration of various features (e.g. permission concept, exports and submission to INSDC) into MetaBar resulted in a complexity of the tool, that possibly scares off potential users. Though detailed documentation how to use the tool is available, experience collected at the MarMic introductory courses on Sylt, showed that an expert needs a couple of days to teach novices in the usage of MetaBar. Though the contextual data that is captured with MetaBar can be prepared for submission to the INSDC, this was not the primary focus of the tool and the integration of this feature has been done towards the end of the MetaBar development phase. These observations motivated the development of the follow-up tool CDinFusion, with a clear focus on sequence and contextual data submission to the INSDC. It was aimed to avoid many of the negative effects described above, which potentially hamper the impact of such a tool. Since it is required by journals that biologist who analyze sequence data in publications have to submit their data to INSDC, it puts no extra burden to the biologists to prepare these submissions. 1 This number is not including access from PubMed Central or other archive sites.
7.2. GSC standards development 89 This holds true, if the tool succeeds to do this in a straightforward and easy manner. CDinFusion does not implement a user management. No authentication, logins or passwords are required. Still, CDinFusion - as a web-based tool - can be used in parallel by many users in separate sessions. The workflow of the tool has been reduced to a neccessary minimum. It should qualify to be easy and straightforward. The documentation of the tool has been improved with a seven minute online video tutorial that covers the complete functionality of the tool. The open source code base is readily accessible and can be easily installed. The future will show, if this tool will be accepted by the community. 7.2 GSC standards development The design, development and publication of the MIMARKS standard coincides with the duration of this thesis. After the initial talk at the 6th GSC meeting in October 2008, which started the development of the MIENS standard (later renamed to MIMARKS) under the lead of the MPI in Bremen, the standard was discussed, changed, improved and extended by the GSC community. For this thesis the development of the MIMARKS standard and the implementation of MetaBar and CDinFusion was a complementary process. The MIGS/MIMS standard [Field et al., 2008] was finished and published during the early implementation phase of MetaBar. The MIMARKS standard was still in development. CDinFusion and the MIMARKS standard were developed in parallel. Changes in the standard led to changes in the implementation of the tool. When requirements for standard improvements became apparent they could directly be communicated. This led to refinements of the standard, while it was still in development. For instance, the need for the GSC web service described in section 4.5, was a result of the implementation of the web forms for the GSC parameters in CDinFusion. In first beta tests of the tool it became apparent that users need detailed descriptions about the GSC parameters. The web service that can be used to retrieve all parameters and descriptions of the MIxS parameters from the GSC database was implemented at the same time. The web forms in CDinFusion are now dynamically retrieving the parameter names
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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CHAPTER 2 METABAR A tool for consis
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2.2. Background 23 molecular sequen
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2.2. Background 25 printing of data
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2.4. Results 27 KML export function
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2.4. Results 29 Figure 2.3: Screens
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2.5. Discussion 31 taking samples i
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2.5. Discussion 33 Handlebar MetaBa
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2.6. Conclusion 35 rine Microbiolog
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Page 65 and 66: 4.2. Introduction 57 edge generatio
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
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Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 120 and 121: 112 BIBLIOGRAPHY [Ramette, 2007] Ra
Page 122 and 123: 114 BIBLIOGRAPHY (2006). Microbial
Page 124 and 125: 116 BIBLIOGRAPHY [Williamson et al.
Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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