The German Network for Bioinformatics Infrastructure (de.NBI) – a

The German Network for
Bioinformatics Infrastructure
(de.NBI) – a short overview
Prof. Dr. A. Pühler
de.NBI coordinator
Bielefeld, April 2015
The German Network for Bioinformatics Infrastructure
(de.NBI) – a short overview
Prof. Dr. A. Pühler
de.NBI coordinator
Bielefeld, April 2015
Content
1
Mission statement of the de.NBI project ......................................................................... 2
2
Composition of the de.NBI consortium ........................................................................... 2
3
The development of the de.NBI initiative ........................................................................ 3
4
The organization of the de.NBI project ........................................................................... 4
5
The eight de.NBI service centers .................................................................................... 5
6
The Central Coordination Unit (CCU) ............................................................................. 7
7
The five Special Interest Groups (SIGs) ......................................................................... 9
8
9
7.1
The Special Interest Group SIG 1 “Web Presence” ................................................. 9
7.2
The Special Interest Group SIG 2 “Service and Service Monitoring” ......................10
7.3
The Special Interest Group SIG 3 “Training and Education” ...................................10
7.4
The Special Interest Group SIG 4 “Infrastructure and Data Management” ..............11
7.5
The Special Interest Group SIG 5 “de.NBI Development” .......................................11
The de.NBI Coordination and Administration Unit (CAU) ...............................................11
8.1
The de.NBI Coordinator .........................................................................................11
8.2
The de.NBI Administration Office ...........................................................................12
The de.NBI Scientific Advisory Board (SAB)..................................................................12
10 References ....................................................................................................................13
1
1
Mission statement of the de.NBI project
i.
The ‘German Network for Bioinformatics Infrastructure’ provides comprehensive firstclass bioinformatics services to users in basic and applied life sciences research.
ii.
The de.NBI program coordinates bioinformatics training and education in Germany.
iii.
The de.NBI program coordinates the cooperation of the German bioinformatics
community with international bioinformatics network structures.
Figure 1: The mission statement of the de.NBI project
2 Composition of the de.NBI consortium
The de.NBI consortium consists of 23 project partners
which are organized in 8 service centers. The
locations of the project partners and service centers
are shown in Fig. 2. The internal structure of each
individual service center is presented in Table 1.
Figure 2: Locations of project partners and service centers of the de.NBI initiative
2
Table 1: Internal structure of the de.NBI service centers
Center
Coordinator
(A) ’Heidelberg Center for Human Bioinformatics (HD-HuB)’
R. Eils,
Heidelberg
Partners: - DKFZ Heidelberg
- EMBL Heidelberg
- Universität Heidelberg
(B) ‘Bielefeld-Gießen Center for Microbial Bioinformatics (BiGi)’
Partners: - Universität Bielefeld
- Universität Gießen
(C) ‘Bioinformatics for Proteomics (BioInfra.Prot)’
Partners: - Medizinisches Proteom-Center der Universität Bochum
- Leibniz-Institut für Analytische Wissenschaften – ISAS e.V. Dortmund
(D) ‘Center for Integrative Bioinformatics (CIBI)’
Partners: - Freie Universität Berlin
- Universität Konstanz
- Universität Tübingen
(E) ‘RNA Bioinformatics Center (RBC)’
Partners: - Universität Freiburg
- Universität Leipzig
- Max-Delbrück-Zentrum für Molekulare Medizin Berlin
(F) ‘German Crop BioGreenformatics Network (GCBN)’
Partners: - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben
- Helmholtz-Zentrum München
- Forschungszentrum Jülich
(G) ‘Database Node’
Partners: - Jacobs University Bremen - SILVA
- Universität Bremen - PANGAEA
- Leibniz-Institut DSMZ Braunschweig - BacDive
- TU Braunschweig - BRENDA
(H) ‘Data Management Node (NBI-SysBio)’
Partners: - HITS Heidelberger Institut für Theoretische Studien
- Universität Rostock
J. Stoye,
Bielefeld
M. Eisenacher,
Bochum
O. Kohlbacher,
Tübingen
R. Backofen,
Freiburg
U. Scholz,
Gatersleben
F. O. Glöckner,
Bremen
W. Müller,
Heidelberg
3 The development of the de.NBI initiative
The first step in establishing a German Network for Bioinformatics Infrastructure was initiated
by the Bioeconomy Council publishing a statement in April 2012 entitled “Requirements for a
Bioinformatics Infrastructure in Germany for future research with bioeconomic relevance” [1].
This statement was presented to the Federal Ministry of Education and Research (BMBF). In
May 2013 the BMBF published an announcement [2] for the selection of service centers
which should form the basis for a bioinformatics infrastructure in Germany. In October 2013,
finally, an international evaluation panel selected eight service centers which were asked to
form a German Network for Bioinformatics Infrastructure (de.NBI) by developing a joint
3
proposal during a conceptional phase. In order to structure the conceptional phase a
coordinator for the de.NBI project was appointed by the BMBF in January 2014 and an
administration office was established in February 2014. During the first months of the year
2014 the joint application was completed and approved again by the evaluation panel. The
de.NBI project was finally started on March 1, 2015.
4 The organization of the de.NBI project
The organigram of the de.NBI project is presented in Figure 3. The Central Coordination Unit
(CCU) is the decision taking body of de.NBI. The CCU consists of nine delegates; eight
delegates are nominated by the service centers. One additional seat is reserved for the
de.NBI coordinator. The CCU can arrange so called Special Interest Groups (SIGs) which
are responsible for providing solutions concerning special questions to be treated in CCU
meetings. The organization of CCU meetings is tin the hand of the Coordination and
Administration unit (CAU). There is also a Scientific Advisory Board (SAB) which interacts
with the coordinator, the Central Coordination Unit and the service centers.
Figure 3: Organizational chart of the de.NBI project
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5 The eight de.NBI service centers
A brief overview on the research topics and the related services offered by the de.NBI
service centers are presented in Fig. 4. It should be mentioned that three service centers
deal with medical, microbial and plant genomics. Two service centers are involved in
proteomics and RNA bioinformatics. One service center is specialized in integrative bioinformatics. The last two service centers concentrate on data management and data collection.
Figure 4: Overview of the research topics and the related services offered by the units
of the ‘German Network for Bioinformatics Infrastructure (de.NBI)’. Each unit of the
network, including six service centers (red) and two local data resource nodes (green,
blue), provides bioinformatics services in a defined field of scientific expertise,
thereby covering many areas of life sciences research.
A more detailed description of the eight de.NBI service centers is given below.
(A)
The ’Heidelberg Center for Human Bioinformatics (HD-HuB)’ provides access to
state-of-the art bioinformatics infrastructure and know-how in the key application
areas of human genetics and genomics, human microbiomics and systematic pheno5
typing of human cells. A special field of expertise of the HD-HuB partners DKFZ,
EMBL and Heidelberg University lies in the area of analysis of next-generation
sequencing data with its tremendous potential for biomedical research.
(B)
The ‘Bielefeld-Gießen Center for Microbial Bioinformatics (BiGi)’ combines the
bioinformatics expertise and resource facilities at Bielefeld University and Gießen
University as required in the field of microbial genome and post-genome research.
The center builds on the collective expertise available in the areas of terrestrial, plant,
food, animal, and clinical microbiology and includes recent developments in the field
of synthetic microbiology.
(C)
The Service Center ‘Bioinformatics for Proteomics (BioInfra.Prot)’ is composed of
the Bioinformatics/Biostatistics work group of the Medizinisches Proteom-Center
Bochum and the Department of Bioanalytics of the Leibniz-Institut für Analytische
Wissenschaften - ISAS - e.V. The BioInfra.Prot center focuses on bioinformatics for
proteomics and on bioinformatics for human and medical/clinical data. The unit has
deep experience with proteomics tools and proteomics standards and analyses in the
field of clinical and human proteomics.
(D)
The ‘Center for Integrative Bioinformatics (CIBI)’ joins the expertise from research
groups of the Freie Universität Berlin, Universität Konstanz and Eberhard-KarlsUniversität Tübingen that have developed valuable bioinformatics resources for nextgeneration sequencing analysis, proteomics, metabolomics, and scientific workflows.
CIBI will be an important resource for integrative bioinformatics and its application
fields, offering sustainable software solutions in the form of libraries, tools and
workflows.
(E)
The ‘RNA Bioinformatics Center (RBC)’ with research partners from the universities
of Freiburg and Leipzig and the Max Delbrück Center for Molecular Medicine serves
as a contact point for RNA bioinformatic enquiries. The center provides specialized
curated RNA-related information resources and services or expertise in topics like
RNA structure analysis, prediction of ncRNA targets, definition and classification of
RNA transcripts, and the analysis of protein-RNA interactions.
(F)
The ‘German Crop BioGreenformatics Network (GCBN)’ provides tailored plantspecific data and infrastructure to the plant research and plant breeding community.
The partners from Crop Plant Research at Gatersleben, the Helmholtz Center Munich
and the Forschungszentrum Jülich are internationally leading in the implementation
and development of plant genome oriented bioinformatics and provide expertise in
the statistical analysis and the interpretation of quantitative transcriptomic data. The
‘Leibniz Institute of Plant Genetics and Crop Plant Research’ maintains the Federal
Genebank of Agricultural and Horticultural Crop Species.
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(G)
The ‘Database Node’ consists of the four databases SILVA, PANGAEA, BacDive,
and BRENDA with quality-controlled reference datasets. These local data resources
provide access to and services for ribosomal RNA genes from all three domains of life
(SILVA), georeferenced data from earth system research (PANGAEA), strain-linked
information on the different aspects of bacterial and archaeal biodiversity (BacDive),
and comprehensive enzyme information (BRENDA). Serving users in academia and
industry is the core mission of the database node. All databases reflect the core expertise of their home institutes in Bremen and Braunschweig.
(H)
The ‘Data Management Node (NBI-SysBio)’ provides bioinformatics support and a
standards-based data management for systems biology projects, with focus on the
provenance of experimental results and on the reproducibility of modeling experiments, as well as high-quality curated biochemical data to modelers and experimentalists. The node concentrates on two tools for the data management in life sciences
research: SEEK, a catalogue for storage, registration and exchange of data and
models; and SABIO-RK, a data repository for biochemical reaction kinetics.
6 The Central Coordination Unit (CCU)
The management of scientific, technical and administrative aspects of the de.NBI consortium
is the mandate of the Central Coordination Unit (CCU). Hence, the CCU is the main decisionmaking body of de.NBI and responsible for the effective operation of the scientific, technical
and administrative management structure (see Table 2). The principal mission of the CCU includes: (i) defining the scientific strategy of de.NBI and the internal procedures to achieve the
de.NBI goals, with particular focus on recent scientific advances and breakthroughs; (ii)
measuring the progress and success of services and outputs defined in the work packages
of the de.NBI partners, with particular focus on the avoidance of overlapping activities; (iii)
evaluation of the user quantification and the user acceptance of the de.NBI services; (iv) assessing the end users’ needs and feedbacks to permanently improve the de.NBI services; (v)
establishing and monitoring measures for quality control and quality assurance of the
network structures and services; (vi) conceiving concepts for national and international networking strategies of de.NBI; (vii) conceiving concepts for the connection of de.NBI to industry; (viii) conceiving concepts for sustainability of the de.NBI services; (ix) conceiving
scientific concepts and recommendations for the strategic amendment of the de.NBI consortium in the course of the second call by the BMBF/Pt Jülich. Each year the CCU convenes a
plenary meeting of the de.NBI staff, preferably as a satellite meeting to the de.NBI workshop,
to discuss all matters related to the de.NBI consortium as a whole.
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The board of the CCU consists of nine de.NBI partners, namely one elected representative
from each de.NBI unit (i.e. the unit coordinator) and the de.NBI coordinator. It is planned to
meet quarterly for regular CCU meetings that are chaired by the de.NBI coordinator and
organized at the institutes of the de.NBI partners in collaboration with the administration
office. The staff members of the administration office take part in the CCU meetings as
guests. The efficient functioning of the CCU is defined by general rules of internal procedure
to be conceptualized by the CCU board at the initial meeting. This compilation of general
rules is a fundamental basis for governing meetings and other scientific and administrative
operations of the CCU and the de.NBI consortium. The rules of internal procedure are
supplemented by a consortium agreement between the institutes of all de.NBI partners,
providing a legal business document outlining the basic terms of scientific collaboration
within de.NBI, each party’s responsibilities and any additional warranties or promises.
Moreover, the consortium agreement is a legal document for all de.NBI partners to confirm
the acceptance of the organization and management structure of de.NBI and, in particular, all
items related to scientific and financial reports to be provided to the BMBF/Pt Jülich.
Table 2: Tasks of the Central Coordination Unit (CCU) – In brief

Establishing procedural rules for the CCU and the de.NBI consortium

Developing a consortium agreement for all de.NBI partners

Discussing and deciding on strategic goals of de.NBI, like

o
development of training and education concepts
o
development of guidelines for the cooperation with industry
o
development o a concept for sustainability
Discussing the development of contacts to existing national and international
bioinformatics networks

Controlling the project aims of the de.NBI partners as defined in the workpackages

Approving the periodical reports for the BMBF/PtJ Jülich and the SAB
Supporting work of the CCU is contributed by subcommittees denominated Special Interest
Groups (SIGs) focusing on various scientific topics relevant for operational and strategic
decisions by the de.NBI management. SIGs are small discussion groups of de.NBI experts.
SIG meetings are chaired by a de.NBI partner nominated by the CCU. Protocols of the
meetings and compiled recommendations of the SIGs are transmitted to the CCU for further
discussion and deliberation. The CCU can establish either temporary SIGs on specific issues
or permanent SIGs on perpetual outstanding issues of de.NBI. It is currently planned to
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establish five SIGs: SIG Web presence; SIG Service and Service Monitoring; SIG Training
and Education; SIG Infrastructure and Data Management; SIG de.NBI Development.
7 The five Special Interest Groups (SIGs)
SIGs are small discussion groups of de.NBI experts or representatives from all de.NBI units
and are established by the CCU. Meetings of the SIGs are generally chaired by a member of
the CCU and are attended by a member of the Coordination and Administration Unit.
Protocols of the meetings and compiled recommendations of the SIGs are presented to the
CCU for further discussion and deliberation. It is planned that SIG meetings will take place
four times per year, at least in the early stages of the establishment phase of de.NBI. SIGs
are an optimal instrument of the CCU to cover and handle more or less all open questions of
the review panel related to operational and strategic tasks of the de.NBI management. This
instrument is improved in such a way that each SIG can make recommendations to allocate
work connected to the important de.NBI tasks service and education to the different de.NBI
units.
7.1
The Special Interest Group SIG 1 “Web Presence”
The SIG Web presence takes care of developing a concept for one common website. This
SIG will continue the work already started during the design phase of de.NBI by members of
the writing team. It is currently planned to charge a professional website design service for
creating a modern web presence, including the website design, corporate design, and logo
design. This common website will include general information on the de.NBI consortium and
detailed information for users on the de.NBI services, the training and education program,
other de.NBI activities, user feedback and discussion fora, and contact details (“hotlines”).
The common website of the de.NBI consortium will also include detailed information on how
to get access to and how use the de.NBI services, and on how to participate in the de.NBI
training and education program. As part of the central web presence, social media will be
explored as a dissemination tool. Using Twitter and Facebook can be very effective to push
out short updates on the status of the services and on updates and releases. What will be
available for the user is clearly outlined by each de.NBI partner in the concept of the project.
It is the explicit mandate of the de.NBI personnel to provide the services at the individual
service centers and to organize and conduct training and education activities. The expert
representative for services at the AO will take care of the maintenance and future
development of the website in collaboration with the SIG Web presence and the de.NBI
partners.
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7.2
The Special Interest Group SIG 2 “Service and Service Monitoring”
The central de.NBI website will include overviews of the software tools, databases, web
servers, computing facilities, and other services offered by de.NBI. The SIG Service and
service monitoring will take care that all services are intuitively presented and documented
on the website. The SIG will develop a general workflow and guidelines for handling user
requests for the various offered services of de.NBI.
As outlined in the de.NBI project concept, user numbers and the user acceptance of the services are only measurable with a set of different parameters when considering the various
user profiles and the variety of services provided by the de.NBI units. The concept of the
project presents an allocation of selected parameters to five alternative types of services and
a monitoring scheme for user numbers and the user acceptance. Therefore, each de.NBI unit
selects the best fitting parameters for each of the provided services to start a continuous
monitoring at the beginning of the establishment phase and to define in this way the base
line of user numbers. The continuous monitoring of user numbers or usage statistics is
complemented by additional measures to assess customer satisfaction. The feedback of
users is collected decentralized at the service centers after the delivery of the services and in
the central user feedback forum on the common website. User meetings arranged by the
service units, for instance in the course of training and education, are additional effective
means to collect the user feedback on specific services. All these items are handled by the
SIG Service and service monitoring. It also takes care of establishing effective procedures to
record and evaluate the feedback of users. Detailed usage statistics and end-user statements about the service quality and ease of use are provided for the mid-term review.
7.3
The Special Interest Group SIG 3 “Training and Education”
The de.NBI consortium will develop an integrated educational concept to coordinate the different activities of the de.NBI partners and to ensure the harmonious functioning of the services in the field of education and training, as an integrated concept has clear advantages
over non-coordinated teaching of related subjects. Detailed concepts for integrated training
and education will be developed by the SIG Education. The resulting training and education
plan of the de.NBI consortium will be displayed on the common website. However, integrated
training remains a form of traditional teaching and is sometimes less conductive to efficient
learning than educational activities designed to help the user and lead him to achieve the
necessary integration by his own efforts. Therefore, the de.NBI concept will of course contain
additional activities exceeding the standard training courses and will make use of the wide
range of teaching and service activities via the internet.
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7.4
The Special Interest Group SIG 4 “Infrastructure and Data Management”
The de.NBI consortium will take care of developing and implementing technical standards to
maximize compatibility, interoperability, safety, repeatability, and quality of the services. The
SIG Infrastructure and data management will delineate a catalogue of harmonized standards
(e.g. standard data formats) and guidelines (e.g. SOPs or minimal information documents)
for the de.NBI units, including rules for the handling and the release of data and the hand-off
of datasets to public data repositories. As de.NBI offers services for users in life sciences
research, these users are in general the owners of the data and hence only the users/owners
can authorize a data release. It is self-evident that the members of the de.NBI consortium
follow all national and international regulations, in particular laws governing data protection
and data security when handling clinical data, if handling is at all legally possible. Moreover,
the de.NBI consortium will adhere to all requirements as detailed in the ethics approval of the
particular project.
7.5
The Special Interest Group SIG 5 “de.NBI Development”
The SIG de.NBI development supports the management of administrative, scientific and
technical aspects of the de.NBI consortium. It will also assess the prospects for the national
and international cooperation of de.NBI with other bioinformatics network structures and
research networks, subject to agreement by the BMBF. The SIG de.NBI development will
also support the process of communicating the value of de.NBI services to customers for the
purpose of selling these services, in particular to customers from industry. It will moreover
develop marketing concepts for customer relationship management. Furthermore, the need
for integration of new services into de.NBI will be assessed in the future.
8 The de.NBI Coordination and Administration Unit (CAU)
8.1
The de.NBI Coordinator
The distinguished mission of the de.NBI coordinator appointed by the BMBF is the building of
the overall de.NBI service network and its scientific integration into prominent national and
international bioinformatics network structures. The de.NBI coordinator is the chairman and a
voting member of the Central Coordination Unit (see 6) and is responsible for the overall
organization, the management structure and the shaping of future scientific strategies of
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de.NBI. The collaboration between the de.NBI coordinator and the Central Coordination Unit
(CCU) will be defined by the CCU in internal rules of procedure. The de.NBI coordinator is
the highest institution of the de.NBI consortium and represents the interests of the de.NBI
partners to third parties. The de.NBI coordinator is the person to contact by the chairman and
members of the scientific advisory board (see 9), the BMBF/Pt Jülich, and other official
bodies in the course of national and international networking. It is the responsibility of the
de.NBI coordinator to control the scientific workflow within the de.NBI consortium and to
ensure accurate delivery of reports to the scientific advisory board and the BMBF/Pt Jülich.
8.2
The de.NBI Administration Office
The de.NBI Administration Office (AO) is part of the Central Administration Unit (CAU) and
the central support entity for de.NBI coordinator and the Central Coordination Unit (Fig. 3). It
provides a range of administrative and management services to the consortium and serves
as a connecting point between the de.NBI coordinator and the Central Coordination Unit. The
AO facilitates the communication within the de.NBI consortium, with users of de.NBI services
and the public on behalf of the de.NBI coordinator and the Central Coordination Unit. The AO
works to build and sustain relationships with users of de.NBI services, industrial partners and
offices that may coordinate related regional, national or international activities. The staff of
the AO (in collaboration with the Special Interest Group Web Presence (see 7.1) is
responsible for maintaining a de.NBI web page to bring together in a uniform way the mission
and organization of de.NBI, the scientific information related to services by the de.NBI
partners, schedules regarding bioinformatics training, education and scientific activities, and
guidelines for academic and industrial users of de.NBI services.
9 The de.NBI Scientific Advisory Board (SAB)
The Scientific Advisory Board (SAB) of de.NBI is independently established by the BMBF
and provided with a broad mandate to advise the de.NBI partners and in particular the
Central Coordination Unit on technical, organizational and strategic matters related to the
de.NBI goals. The principal mission of the SAB is summarized in Table 3. Evaluation of the
de.NBI consortium by the SAB is scheduled as an annual process that is associated to the
internal de.NBI workshop. It is planned that the Central Coordination Unit provides the BMBF
with a list of national and international candidate experts to serve as committee members of
the SAB. The scientific members of the SAB (up to 6 independent experts) are nominated by
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the BMBF. The elected chairman of the SAB directly reports to the BMBF. The board should
be appointed at the beginning of the establishment phase of de.NBI.
Table 3: Tasks of the Scientific Advisory Board – In brief:

Advising the CCU on science, technology and economic issues

Advising the CCU on technical, organizational and strategic matters

Reviewing the scientific and technical development of the de.NBI services

Reviewing the technical basis and infrastructure of the de.NBI partners

Identifying and reallocating scientific needs and services

Reporting decisions and recommendations to the CCU and the BMBF/PtJ Jülich
10 References
[1] Anforderungen an eine Bioinformatik-Infrastruktur in Deutschland zur Durchführung von
Bioökonomierelevanter Forschung, Empfehlungen des Bioökonomierats 06 (2012)
http://www.biooekonomierat.de/publikationen.html?tx_rsmpublications_pi1[publication]=7&tx_rsm
publications_pi1[action]=show&tx_rsmpublications_pi1[controller]=Publication&cHash=d4769cfce
e403d5ac8f14b01c3b3930d
English Version: Requirements for a Bioinformatics Infrastructure in Germany for future
Research with bio-economic Relevance (PDF, 590 kb)
[2] Bekanntmachung: Deutsches Netzwerk für Bioinformatik-Infrastruktur Deutsches
Netzwerk für Bioinformatik-Infrastruktur (Englisch) (PDF - 166 KB)
https://www.ptj.de/nbi
Contact:
Prof. Dr. Alfred Pühler
Coordinator
de.NBI - German Network for Bioinformatics Infrastructure
Center for Biotechnology (CeBiTec)
Bielefeld University
33594 Bielefeld
Phone: +49 521 106 8750
Fax: +49 521 106 89046
e-mail: [email protected]
Förderkennzeichen 031A532 - 031A540
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