Bioinformatics in Austria: Perspectives and Strategy

Outline

0. Executive Summary
1. Background
2. Challenges
3. Solutions
4. Appendix
4.1 Bioinformatics researchers in Austria
4.2 Need matching: A case study of Bioinformatics and Biobanking
4.3 Benefits to Austria of membership of ELIXIR

0. Executive Summary

Bioinformatics is an interdisciplinary field at the interface between computer science and the life sciences, with important applications in basic and applied research for topical areas like molecular medicine, healthy living, agriculture, biotechnology, green energy, etc. Bioinformatics provides the information infrastructure with which these fields analyse their vastly growing repertoire of molecular data. Moreover, Bioinformatics is also becoming the data science and integration science that yields important new discoveries and thereby leverages society’s investment into the life sciences. For these reasons, and like in any other country with strong biomedical research, bioinformatics is of strategic importance to basic and applied research in Austria.

To realize the positive impact of bioinformatics in the life sciences and to overcome the current bottlenecks in data interpretation and utilization, substantial challenges are ahead of us: building national capacities for research, development and training in all areas of bioinformatics, establishing the necessary capacities of computational resources for life science information, and ensuring the sustainability and visibility of resources developed in Austria.

The challenges can be addressed effectively and cost-efficiently only through coordination, collaboration, and network building. We, a group of 70 researchers and practitioners covering all areas of bioinformatics in Austria, thus recommend the formation of a distributed and networked Platform for Bioinformatics in Austria. Similar to the Swiss Institute of Bioinformatics (SIB), this platform will coordinate and network our resources, expertise, and infrastructure for world-leading quality and visibility. It will foster excellence in bioinformatics research and its many applications. It will also facilitate enhancements and new capabilities for life sciences research, development, and industry in Austria.

The proposed Platform for Bioinformatics should be established as independent non-profit foundation recognized of public utility, in order to provide services and exchange for all bioinformaticians. The Platform will maintain strong relations to international organizations in the computational life sciences. Reflecting the key role of bioinformatics in the life science, that is only bound to further increase in the near future, we recommend strong collaboration in training of all stakeholders in Austria. Such collaboration should thus be established across sectors, between universities, institutes, and companies. Training activities are needed at “user” and “specialist” levels, which will also require collaboration between different sites in Austria.

A powerful infrastructure for life-science information in Austria can only be established in integration with national and international research infrastructures. Along with the formation of a Platform for Bioinformatics in Austria, we recommend that Austria should join ELIXIR, Europe’s research infrastructure initiative for life-science data and information. Beneficial activities of ELIXIR include its scientific programme, joint fund raising, technical coordination, industry support, and pilot actions. ELIXIR also supports bioinformatics communities by the definition of core data resources, named services, and the tools and service registry. Austria’s membership in ELIXIR should be complemented by a close collaboration of the Bioinformatics Platform in Austria with all relevant national and international research infrastructures elsewhere, such as the BBMRI-ERIC and de-NBI.

1. Background

1.1 Bioinformatics

Bioinformatics is an interdisciplinary science at the interface between the life sciences and computer science. Bioinformatics became widely recognized when bioinformaticians solved key problems in one of the greatest scientific endeavours – the deciphering of the entire human genome.  Bioinformatics is established today as an independent scientific field in teaching and research. Complex 'big data' from life sciences, such as biology, medicine, pharmacology, and ecology are stored, organized, analysed, compared, and interpreted, and the integrated results visualized by using bioinformatics methods. Bioinformaticians develop and utilize computational algorithms and methods for solving problems from the life sciences. To this end, adjacent fields, such as biomathematics, biostatistics, medical informatics, and laboratory information technology, complement and support bioinformatics.

Bioinformatics researchers approach the research topics from different angles. The “user” perspective is characterized by solving life science problems by application of existing bioinformatics methods, and their combination, improvement and evaluation. Bioinformaticians working this way are often embedded in research facilities or industrial workgroups that generate large-scale data and operate experimental facilities allowing to directly test computational predictions. However, the scientific productivity and success of researchers having this “user” perspective relies on two other branches of bioinformatics: dedicated “method developers” and “resource maintainers”. These are specialists who develop novel algorithms and implementations, collect and organize large-scale life-science data, and develop novel resources and tools. Although method developers and resource maintainers can also be “embedded bioinformaticians”, these are mainly working in dedicated bioinformatics workgroups and institutes.

Technological advances in the life sciences are generating ever more data, bringing bioinformatics to the centre-stage. DNA sequencing, mass spectroscopy, and imaging techniques are increasingly ubiquitous in many areas of biology and medicine. Consequently, ambitious upcoming research areas, such as in personalized health and nutrition, microbiome research, bioenergy, and many more, will require a vital and powerful bioinformatics infrastructure capable of managing huge volumes of life-science information at the highest scientific levels.

1.2 Setting the scene

Many representatives of the Austrian bioinformatics community have met at the symposium "Austrian infrastructure for life-science information" on March 24, 2015. At this meeting it was decided to develop this whitepaper, defining a future strategy for bioinformatics in Austria. We have established an initial collaborative platform for exchange of material and information. This online portal connects the community and functions as a seed for the recommended Bioinformatics Platform.

We below provide a brief survey of the bioinformatics scene in Austrian research, industry, and education.

Vienna area:

Bioinformatics institutes or workgroups exist at the universities in Vienna (University of Vienna, Technical University, Medical University, University of Veterinary Medicine, University of Natural Resources and Life Sciences ‘Boku’), at the biology institutes of the Austrian Academy of Science (CeMM, GMI, IMBA), at the Research Institute of Molecular Pathology (IMP), at the Institute of Science and Technology Austria (ISTA), at the Austrian Institute of Technology (AIT), and at the Campus Science Support Facilities (CSF) of the Vienna Biocenter. Internationally visible scientific strengths comprise (among others) the calibration of quantitative assays, applications and method development in RNA bioinformatics, molecular evolution, population genetics, biomedical genomics/epigenomics, and host-microbe interactions. The groups maintain multiple connections mainly in education (collaboration within and between institutions) and research (joint projects).

Graz:

In the last year, two Professorships for Bioinformatics and Computational Biotechnology, respectively have been established at the TU Graz. An additional Professorship for Bioinformatics is currently being recruited to the Karl-Franzens Universität. Currently existing institutes/departments with bioinformatics competence at the Medical University Graz are the Institute for Medical Informatics, Statistics and Documentation and the Core Facility for Computational Bioanalytics at the Center for Medical research.

Innsbruck:

The Medical University of Innsbruck established a professorship for bioinformatics in 2010 and built up a computational infrastructure to support the local community including NGS data analyses. The Medical University of Innsbruck coordinates a prestigious Horizon2020 project (APERIM: Advanced bioinformatics methods for personalized cancer immunotherapy).

Linz area:

The main bioinformatics workgroups and institutes are represented by the Institute of Bioinformatics, Johannes Kepler University Linz, and in the Bioinformatics Research Group, University of Applied Sciences Hagenberg.

Salzburg:

Bioinformatics research groups are established within the Division of Structural Biology and Bioinformatics and the Department of Molecular Biology of the University of Salzburg.

2. Challenges

2.1 Competence and training

A key challenge is providing project-specific, user-centric training, typically for scientists post graduation. The target audience is bench scientists who need to know where to store their data, how to correctly process and analyse it, and how to comprehensively interpret results. Austria therefore needs to build up its capacity in Bioinformatics training, which plays a fundamental role in supporting many users across the life sciences such as biologists, bench scientists, geneticists, biochemists, clinical specialists, and plant, environmental and marine scientists. In the future even clinicians may require basic bioinformatics training. Following the rapid progress and developments in bioinformatics, as well as the different needs in different areas of life sciences, such training should be specific and problem-oriented. This sector is underdeveloped in Austria and therefore needs special attention.

Method and resource development in Bioinformatics are fields for specialists, working at the interface between very different disciplines. Talented researchers in this field have been and are still a rare breed. They are subject to tough international competition, not only between different institutions, sites and countries, but also between academia and industry. Excellent bioinformaticians are actively searched worldwide and offered attractive packages. Austria has recognized this in principle: The 2015 call of the Vienna Science and Technology Fund (WWTF) for an excellent young researcher from abroad for the set-up and management of an independent research group in computational bioscience represents a typical example. Furthermore, in order to sustain lively, internationally competitive and successful bioinformatics groups, we need to create an environment that fosters and retains the top Bioinformatics researchers and educators in Austria. Without this, the best talent growing in Austria will move elsewhere, a painful loss of investment for our research environment. It is particularly in this area that the current setup falls short, and considerable action is urgently required. It is noteworthy that this is also recognized elsewhere, with the German Society for Bioinformatics (FaBI) in their latest position paper making a strong push in this direction.

Training of new researchers in Bioinformatics is particularly challenging due to the interdisciplinary nature of the field and its rapid development. Undergraduate education at universities and universities of applied sciences dominates traditional bioinformatics training, and is complemented by post-graduate training and special paths for career changers. Bioinformatics training needs to be differently focused on two distinct audiences. Users of bioinformatics methods require sound understanding of the basic principles, assumptions, and limitations of computational methods in the life sciences. Many universities therefore offer bioinformatics training as part of their biology, ecology, medicine, and pharmacy curricula. The training of Bioinformaticians with method development and resource maintenance skills, however, requires particular curricula for bioinformatics. Students are trained in the relevant subjects of computer science (e.g., algorithms, software development, databases), mathematics and statistics, and learn to understand and solve computational problems in the life sciences. It is noteworthy that Bioinformatics as a heterogeneous discipline has grown to the point that early specialization is essential for achieving sufficient depth in the typically shorter post-graduate courses. Teaching of specific topics and developing specific problem-solving skills in bioinformatics should thus make up a substantial fraction of bioinformatics curricula. Therefore, there is a need to keep developing cutting-edge Bioinformatics curricula, whereas bioinformatics curricula that are just combinations of life science and computer sciences lectures usually don’t succeed.

2.2 Computational resources

Most Bioinformatics groups operate or have some access to specialized high-performance computing (HPC) infrastructure for computational life science. The main difference to traditional HPC facilities that are primarily geared at physics, astronomy, and climate sciences is the equipment with dedicated hardware suitable for Big Data science, complemented by a rich, flexible, and up-to-date bioinformatics software repository and the availability of major biological databases on-site. Such an installation allows users to analyse their data effectively.

Bioinformatics infrastructure on one hand needs to be friendly to non-specialists, while supporting both production data analysis as well as method development and evaluation. The typical operational model for Bioinformatics is full-time operation with a critical need for short queuing times. This is more important than highest availability, as the data need to be analysed iteratively, and in many cases over several years (the duration of the project). The exponential growth of data volumes in the life sciences is clearly steeper than Moore’s law of doubling CPU capacities every 18 month. While this requires a upgrade cycles of computing hardware and storage at least every 3-5 years minimum, it also emphasizes the critical need for new algorithms and methods development in both industry and academia.

In academia the typical HPC infrastructure for Bioinformatics is often based on medium-sized compute clusters. They consist of head nodes for job testing and submission, compute nodes, and a fast storage cluster. Copies of all relevant biological databases (usually in the range of Terabytes) need to be available as local copies on high-speed disks in all compute nodes, in order to prevent bottlenecks in the network. Such clusters usually operate dedicated database servers and redundant virtualization servers. Virtual machines are mainly used for publicly available resources, such as web portals, databases and tools. Group-based HPC infrastructures are typically not only available for a bioinformatics group itself, but also to other departments and to collaboration partners. To this end, the operating groups not only provide access to bioinformatics HPC facilities, but also provide software and scientific support for the users. Thereby they fulfil a crucial role in establishing local research infrastructure for life science information. In addition to generic computing hardware, dedicated systems (such as DeCyPher TimeLogic boards) are sometimes used, mainly to hardware-accelerate time-critical steps in the analysis, such as database searches or the creation of phylogenetic trees for all genes of an entire genome.

However, in Austria, external funding for hardware, software, administration, and user support is usually not easily available – making it challenging for Bioinformatics groups to sustain these facilities in the long run. Therefore joint activities have been launched, such as the recent HRSM project of several universities establishing mid- and high-memory computing nodes and fast central temporary working storage in stage-3 of the Vienna Scientific Cluster (VSC-3). This investment in hardware to support Big Data science has been a crucial stepping-stone, and will become available to the community in 2016.

The set-up of administrative structures (e.g. Steering Group) to ensure support for an operational model of life science specific HPC resources, that allows the short-latency high-peak usage that is often required in bioinformatics, is pending. Future developments necessarily include the secure archival storage of the original large-scale measurement data and analysis results. Moreover, long-term support for the set-up and maintenance of up-to-date software and database installations will need to be found. In particular, it will also be essential to link larger shared facilities to the highly valuable distributed specialist resources at individual Bioinformatics institutes.

2.3 Sustainability and visibility of resources developed in Austria

Austrian Bioinformaticians working in resource development and maintenance currently experience specific funding challenges. Most often novel, innovative tools and resources are inspired from basic research and are implemented in the course of a research project. After publication of the resource and the end of such projects the authors struggle to sustain it over a longer period, especially when offering computational tools as a Web-based community resource. Funding from own and third-party institutions is usually not available for this purpose. Sustaining public resources over a long time therefore requires substantial initiative and financial resources from the groups themselves. These are often limited; so many interesting bioinformatics resources disappear shortly after their publication or as soon as they become popular enough to be overloaded with external requests.

In Austria currently no infrastructure exists for identifying the strengths of the best resources created here (e.g., via impact factors, usage counts and citation levels). Furthermore, no platform exists through which users could request resources according to their unmet needs. In summary, the lack of a shared infrastructure and funding for long-term maintenance of methods and resources often result in a waste of investment.

3. Solutions

We suggest three primary actions in order to the address the challenges described above. These will not only be beneficial for bioinformatics but will also of strategic importance for entire life science in Austria. We recommend (i) the foundation of a Bioinformatics Platform in Austria, (ii) the collaboration in bioinformatics training and education, and (iii) long-term support of investments into shared infrastructure and resources and their integration with national and international research infrastructures worldwide.

3.1 A distributed and networked Platform for Bioinformatics in Austria

With the end of the GENAU program (Austrian genome research program 2001-2012) also the central networking platform for Austrian Bioinformaticians has disappeared. This program has helped establish the international competitiveness of Austrian genome research and was therefore very important for developing a productive Bioinformatics community. Compared to Switzerland, a similar sized neighbouring country where the Swiss Institute of Bioinformatics (SIB) organizes the national infrastructure in a world-leading quality and visibility, Austria so far lacks a similar institution. We therefore recommend the foundation of a Bioinformatics Platform in Austria. It should be established as a legal entity, allowing it to become a partner for decision-makers in science, industry, and politics.

The platform will foster excellence in Bioinformatics and facilitate a successful future of the life sciences in Austria. It should be established as independent non-profit foundation recognized of public utility. It should be engaged in the efficient coordination of bioinformatics activities in Austria, covering research, education, and procurement of joint funding. It will provide services, exchange, and training for all Bioinformaticians by membership. As supported by future funding, instruments of the platform may include specific scholarships and bursaries for people seeking careers in bioinformatics. Special emphasis would be put on the minimization of redundancy in investments and long-term sustainability.

We recommend a management structure comprising (i) a Board of Directors: defining the platform’s scientific strategy and procedures, (ii) an Executive Director, elected from the Board of Directors and responsible for the overall management of the platform, and (iii) a Scientific Advisory Board, making recommendations on the activities of the platform.

The Platform for Bioinformatics in Austria will further develop and maintain strong relations to international organizations in computational life science, such as the International Society for Computational Biology (ISCB, including national ISCB student groups), ELIXIR, the German Network of Bioinformatics Infrastructure (de.NBI) and others.

3.2 Training, education and career development

We recommend strong collaboration in undergraduate and graduate training in Bioinformatics across different universities, institutes, and companies. Exchange between different locations should be encouraged and of major advantage for the quality and comprehensiveness of curricula. These activities should be complemented by nationwide programs on the post-graduate level, e.g. by an Austrian PhD programme in Bioinformatics, and through thematically focused summer schools. In the interest of training related to practice we would encourage industry to contribute to bioinformatics education and training.

High-quality interactive trainings take a long time to develop. The Platform for Bioinformatics in Austria could thus provide an excellent platform to join forces in computational life sciences trainings by sharing course materials, coordinating training events and building up a truly comprehensive training portfolio that can help experimental scientists to manage and analyse their data much more efficiently.

Talented scientists often leave Austrian universities and research institutions after graduation or completion of their PhD, as they have better career perspectives in other countries or in industry. To stop and invert the current “brain drain” we therefore recommend a higher appraisement of bioinformatics in the funding instruments for career development and in life science related funding calls. The recent call of the WWTF for Vienna Research Group Leaders in Computational Bioscience is an encouraging signal in this context.

3.3 Scientific computing

The Platform for Bioinformatics in Austria should be engaged in establishing excellent scientific and high-performance computing platforms for all research groups in life science in a scalable, sustainable and economical manner. This overall goal encompasses several important aspects:

  • Secure computing and storage capacities for processing original large-scale measurement data and analysis results in life science.
  • Ensure long-term support for the set-up and maintenance of up-to-date software and database installations.
  • Make scientific computing easily accessible by providing user-friendly tools such as analysis pipelines, pre-configured virtual machines, software as a service etc.
  • Provide outstanding user services by offering support to plan in silico experiments, methodological consulting, and trainings.
  • Maintain a state-of-the-art software environment (scientific applications and databases), and complement these tools by custom software development whenever appropriate.
  • Last but not least: achieve these goals in an optimal manner by pooling financial, human and structural resources.

We strongly believe that the best way to achieve these goals is to establish a group of computational and bioinformatics experts within the Platform for Bioinformatics in Austria. This group of experts should develop and synchronize strategies for HPC in life science and should be included in all relevant decision-making to ensure that first-class services will be made available to the life science research community.

3.4 Integration with national and international research infrastructures

We recommend that Austria should join ELIXIR, Europe’s research infrastructure initiative for life-science data and information. Launched in 2014, ELIXIR is a unique, unprecedented initiative to connect Europe’s leading national Bioinformatics centers, services and core resources. Beneficial activities of ELIXIR include its scientific programme, technical coordination, industry support, pilot actions, and opportunities of seeking funding under the framework. Method developers and resource maintainers are also supported by the definition of core data resources, named services, and the tools and service registry.

ELIXIR is a pan-European research infrastructure for biomolecular data. Prioritised by the European Council and ESFRI in 2014 as one of Europe’s three priority new infrastructures, it builds on existing data resources and services and follows a Hub and Nodes model, with a coordinating Hub in Hinxton, Cambridge, and a growing number of Nodes located at centres of excellence throughout Europe (www.elixir-europe.org/about/elixir-nodes). The goal of ELIXIR is to orchestrate the collection, quality control, and archiving of large amounts of biological data produced by life science experiments, and the provision of open access to world-leading data, compute tools, standards, training, and industry services.

At present, eleven countries (Czech Republic, Denmark, Estonia, Finland, Israel, Netherlands, Norway, Portugal, Sweden, Switzerland, UK) and EMBL have ratified the ECA and are full members; a further six countries, (France, Spain, Italy, Slovenia, Greece and Belgium) are Observers and are at various stages of joining as members.

Should Austria join ELIXIR its membership fee for the current period of the ELIXIR programme would be: 2015 - €95,563, 2016 - €101,356, 2017 - €119,286, 2018 - €162,687. The benefits to Austrian of joining ELIXIR are described in the Appendix. We recommend that Austria join as Observer immediately, and aims to seek Full Membership as soon as possible.

Austria’s membership in ELIXIR should be complemented by a close collaboration of the Platform for Bioinformatics in Austria with relevant national and international research infrastructures, iniatiatives, and collaborations, such as:

  • Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-ERIC)
  • Partnership for Advanced Computing in Europe Research Infrastructure (PRACE)
  • German Network of Bioinformatics Intrastructure (de.NBI)
  • Austrian Academic Computer Network (Aconet)
  • Austrian Center for Industrial Biotechnology (ACIB)

According to its national and international importance, we particularly recommend the development of a close collaboration between ELIXIR and BBMRI in Austria as one of the pilot projects of the Platform for Bioinformatics.

Neighbouring countries have already started strengthening their national Bioinformatics infrastructure. In Germany, the new de.NBI Bioinformatics infrastructure funding program by the BMBF started with a first round of funding (22 Million Euros), which will be complemented through several additional rounds of funding over the next 10 years. Similar funding initiatives must be established for Austria to improve and maintain high-performance compute and storage infrastructure. Additional funds for the identification of valuable bioinformatics resources developed in Austria and their long-term maintenance need to be found. The chair of the de.NBI review panel is Prof. Dr. Sensen from the TU Graz. Close connections with de.NBI are therefore also sought, as this initiative is going to lead the Bioinformatics infrastructure development in Germany and its integration into the European network  in the future.

4. Appendix

4.1 Bioinformatics researchers in Austria

Name

Einrichtung

Forschungsthemen

Web

Antonielli Livio

AIT-Austrian Institute of Technology

Microbial community analysis; (Meta-)genome assembly

 

Aszodi Andras

VBCF: Vienna Biocenter Core Facitilies 

theoretical computational biology, high-performance computing, training and teaching

www.csf.ac.at

Berghold Andrea

Institute for Medical Informatics, Statistics and Documentation

RU Statistical Bioinformatics, Genetic epidemiology, Biostatistics and Medical Informatics

 

Birngruber Erich

Gregor Mendel Institute of Molecular Plant Biology GmbH; Dr. Bohr-Gasse 3; 1030 Vienna, Austria

HPC Specialist

www.gmi.oeaw.ac.at

Bock Christoph

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

Medical Epigenomics, Bioinformatics, Single-cell Sequencing, Personal Genomes, Epigenomics

epigenomics.cemm.oeaw.ac.at

Bodrug Alexandrina

University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Bioinformatics Group

Plant genomics, genome sequencing, assembly, high throughput sequencing data analysis

 

Borgmann Daniela

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Dohm Juliane

University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Bioinformatics Group

Plant genomics; genome sequencing, assembly, annotation, biological interpretation; high throughput sequencing data analysis

 

Dorfer Viktoria

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Dorffner Georg

Center for Medical Statistics, Informatics and Intelligent Systems; Medical University of Vienna

Data science for personalized medicine; machine learning and pattern recognition in molecular data; automated quantitative immunohistochemistry

cemsiis.meduniwien.ac.at/ds4pm

Ecker Gerhard

Department of Pharmaceutical Chemistry, University of Vienna

Pharmacoinformatics

pharminfo.univie.ac.at

Egger Bernhard

Institute of Zoology, University of Innsbruck

Assembly, phylogenetics

www.uibk.ac.at/zoology/research/regeneration/

Feichtinger Julia

PostDoc at IMBT Graz, Genome Annotation Pipelines

Tools for Genome Annotation

 

Flamm Christoph

Institute for theoritical chemistry, University of Vienna

 

www.tbi.univie.ac.at/~xtof

Frank Karl

CAME – Center of Applied Molecular Engineering, Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg

Protein structure and sequence

 

Goldmann Daria

Division of Drug Design and Medicinal Chemistry, Dep. of Pharmaceutical Chemistry, University of Vienna

 

pharminfo.univie.ac.at

Graf Alexandra

FH Campus Wien, Department of Applied Life Sciences; ACIB GmbH

Sequence analysis and annotation, Metagenome,

 

Groselj-Strele Andrea Core Facility Computational Bioanalytics, Center for Medical Research, Medical University Graz Research support in applied Biostatistics and Bioinformatics zmf.medunigraz.at

Gruber Christian

Innophore GmbH

Enzyme discovery

www.innophore.com

Gruber Karl

Institute of Molecular Biosciences, University of Graz

Structural bioinformatics, structural biology, molecular modeling

molekularbiologie.uni-graz.at

Gruber Markus

CAME – Center of Applied Molecular Engineering, Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg

Protein structure and sequence

 

Gülly Christian

Center for Medical Research, Medical University of Graz

OMICS technologies

 

Gyenesei Attila

Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities (previously known as CSF)

Next generation sequencing, Data mining, Integrative data analysis

www.csf.ac.at

Hackl Hubert

Biocenter, Division of Bioinformatics, Medical University of Innsbruck

computational genomics, cancer immunology

icbi.at

Hanel Rudolf

Medical University of Vienna, CeMSIIS, Section for Science of Complex Systems

 

www.complex-systems.meduniwien.ac.at/people/rhanel

Hartler Jürgen

PostDoc at IMBT Graz, Tools for MassSpec Analysis

Lipidomics, MassSpec Data Analysis

 

Herbold Craig

DOME-Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna

 

dmes.univie.ac.at

Himmelbauer Heinz

University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Bioinformatics Group

Plant genomics; genome sequencing, assembly, annotation, biological interpretation; high throughput sequencing data analysis

 

Hochreiter Sepp

Institute of Bioinformatics, Johannes Kepler University Linz

Machine learning; Deep learning; Biclustering; Next generation sequencing; Genetics; Genomics; Clinical studies

www.bioinf.jku.at

Hofacker Ivo L.

Institute for theoritical chemistry, University of Vienna

 

www.tbi.univie.ac.at/~ivo

Junttila Sini

VBCF:Vienna Biocenter Core Facilities

RNAseq, non-model organisms

 

Klambauer Günter

Institute of Bioinformatics, Johannes Kepler University Linz

Chemoinformatics; Machine learning; Microarray data analysis; Next generation sequencing;  Copy number variations

www.bioinf.jku.at

Kosiol Carolin

Institute of Population Genetics, Vetmeduni Vienna

 

www.vetmeduni.ac.at/en/population-genetics/forschung/research-groups/kosiol-lab

Kreil David Philip

Department of Biotechnology, University of Natural Resources and Life Sciences, Austria

 

bioinf.boku.ac.at

Lackner Peter

Department of Molecular Biology, University of Salzburg

Protein structure bioinformatics, Immunoinformatics

www.uni-salzburg.at/lackner

Lang Priska

AIT Austrian Institute of Technology

Biostatistics

www.ait.ac.at/themen/bioinformatics/

Lirk Gerald

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Luberacki Borries

Gregor Mendel Institute of Molecular Plant Biology GmbH; Dr. Bohr-Gasse 3; 1030 Vienna, Austria

Lab-Manager / Head of HPC

www.gmi.oeaw.ac.at

McCann Jamie

University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Bioinformatics Group

Plant genomics and population genetics

seq.boku.ac.at/foswiki/bin/view/Home/ProfileJamieMcCann

Menche Jörg

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

Network Medicine, Systems Biology, Molecular Networks, Computational Biology

www.cemm.oeaw.ac.at/research/groups/bioinformatics-joerg-menche

Mohr Thomas

Medical University of Vienna, Institute of Cancer Research / ScienceConsult – DI Thomas Mohr KG

Network Analysis in conjunction with -omics data, Endothelial cells – focus inflammation and angiogenesis

 

Moissl-Eichinger Christine

Internal Medicine, Medical University Graz

Microbiome

www.medunigraz.at/microbiome

Nodine Michael

Gregor Mendel Institute of Molecular Plant Biology

Development; small regulatory RNAs, transcriptomics

www.gmi.oeaw.ac.at/research-groups/michael-nodine

Oostenbrink Chris

University of Natural Resources and Life Sciences Vienna (BOKU),Institute for Molecular Modeling and Simulation

Biomolecular Modeling and Simulation

www.map.boku.ac.at/mms

Pabinger Stephan

AIT Austrian Institute of Technology

Genome sequencing, Genome assembly, NGS, RNASeq, data integration, molecular dynamics simulation, software development

www.ait.ac.at/bioinformatics

Pasterk Markus

BBMRI-ERIC

Biobanking

www.bbmri-eric.eu

Perco Paul

Medical University Innsbruck, Department of Internal Medicine IV

Omics data, biomarker discovery and development, network biology in disease

 

Peters Philipp

University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Bioinformatics Group

Genomics; genome sequencing, assembly, biological interpretation; high throughput sequencing data analysis

https://seq.boku.ac.at/foswiki/bin/view/Home/ProfilePhilippPeters

Peymann Armin

ACIB GmbH (Austrian Center of Industrial Biotechnology)

de novo genome assembly, genome annotation, RNA-Seq data analysis and interpretation, phylogenetic analysis

 

Posch Andreas

Ares Genetics GmbH

Genetic determination of antibiotic resistance

www.ares-genetics.com/

Pröll Karin

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Rattei Thomas

CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna

Microbiome; Microbial symbionts and pathogens; Comparative genomics

cube.univie.ac.at

Rieder Dietmar

Biocenter, Division of Bioinformatics, Medical University of Innsbruck

computational genomics, transcriptional regulation

icbi.at

Schaller Susanne

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Schlick-Steiner Birgit C.

Institute of Ecology, University of Innsbruck

Molecular Ecology

www.uibk.ac.at/ecology/forschung/molecular_ecology.html

Schreiner Wolfgang

Division of Biosimulation and Bioinformatics,  CeMSIIS - Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna

OMICS data analysis for systems medicine; Molecular simulation; Immunoinformatics;Pharmacokinetics

cemsiis.meduniwien.ac.at/en/bsb/research

Schuster Michael

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

Bioinformatics, Next Generation Sequencing, Genomics

biomedical-sequencing.at

Sensen Christoph

Head of IMBT Graz: Genome Annotation, Data Visualization, Virtual Human

Markers for chronic diseases in mammals, Metagenomics, Expressomics

www.tugraz.at/institute/imbt/home

Siehs Christian

FH Technikum Wien, FH Hagenberg, Freiberuflicher Bioinformatiker

medical data analysis, networks and system analysis, bioinformatics, medical informatics, teaching and training

 

Sippl Manfred

CAME – Center of Applied Molecular Engineering, Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg

Protein structure and sequence

 

Soh Jung

Senior Scientist at IMBT Graz, Development of Bioinformatics Tools and Analysis Pipelines for Genomics

Pipeline Development for Large Scale Analyses

 

Steinkellner Georg

ACIB GmbH., Austrian Centre of Industrial Biotechnology, Graz

structural bioinformatics; structural enzymology; molecular modeling and docking; structure

acib.at

Stöggl Wolfgang

Institut für Botanik, Universität Innsbruck

 

 

Sykacek Peter

Department of Biotechnology, University of Natural Resources and Life Sciences, Austria

computational biology in medicine, probalistic modelling, multimodal interference

bioinf.boku.ac.at

Tatto Nadine

ACIB GmbH (Austrian Center of Industrial Biotechnology), FH Campus Wien, Department of Applied Life Sciences

Databases, Genome Browser,

 

Technau Uli

Dept. for Molecular Evolution and Development Centre for Organismal Systems Biology Faculty of Life Sciences University of Vienna

 

molevodevo.univie.ac.at

Thallinger Gerhard

Senior Project Scientist at IMBT Graz, Mostly Lipidomics

Lipidomics

 

Thurner Stefan

Medical University of Vienna, CeMSIIS, Section for Science of Complex Systems

 

www.complex-systems.meduniwien.ac.at/people/sthurner

Trajanoski Slave

Core Facility Computational Bioanalytics, Center for Medical Research, Medical University Graz

Microbiome; Metagenome; RNASeq, CHipSeq, targeted resequencing

zmf.medunigraz.at

Trajanoski Zlatko

Biocenter, Division of Bioinformatics, Medical University of Innsbruck

computational genomics, cancer immunology

icbi.at

Vierlinger Klemens

AIT Austrian Institute of Technology

biostatistics, classification and feature selection, computational genomics, data integration, systems biology

www.ait.ac.at/bioinformatics

Villanova Laura

starts at IMBT in September 2016 as Senior Scientist: Biostatistics

Statistical Analyses, Experimental Design

 

von Haeseler Arndt

CIBIV Max F Perutz Laboratories University of Vienna, Medical University of Vienna.

Phylogenomics, High Throughput Methods, Population biology, Modelling of evolutionary processes

 

Widder Stefanie

CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna

Systems biology of microbial communities/microbiome and gene regulation, process-oriented modeling, network

cube.univie.ac.at

Wiederstein Markus

CAME – Center of Applied Molecular Engineering, Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg

Protein structure and sequence

 

Winkler Stephan

Bioinformatics Research Group-University of Applied Sciences, Upper Austria School for Bioinformatics, Communications and Media, Campus Hagenberg, Dept.of Medical and Bioinformatics

 

research.fh-ooe.at/de/orgunit/842

Wischnitzki Elisabeth

AIT-Austrian Institute of Technology

Transcriptome; Comparative genomics; Comparative transcriptomics; Marker development; GWAS

 

Zanghellini Jürgen

Austrian Biotech University of Applied Sciences; Austrian Centre of Industrial Biotechnology; University of Natural Resources and Life Sciences Vienna (BOKU)

computational systems biology; computational biology; high-performance computing;

www.biotec.boku.ac.at/19055.html

Zatloukal Kurt

Biocenter, Division of Bioinformatics, Medical University of Innsbruck

computational genomics, cancer immunology

icbi.at

Zhou Qi

Dept. for Molecular Evolution and Development Centre for Organismal Systems Biology Faculty of Life Sciences University of Vienna

Sex Chromosome Evolution of Birds and Drosophila

 

Zimmermann Bob

Dept. for Molecular Evolution and Development Centre for Organismal Systems Biology Faculty of Life Sciences University of Vienna

 

molevodevo.univie.ac.at

4.2 Need matching: A case study of Bioinformatics and Biobanking

“Big data” is also a “big topic” in the biological and medical field. Data from a variety of sources as electronic health records, laboratory data, molecular data (gene sequencing, metabolomics, proteomic) as well as patient generated datasets (life style data, medical sensors) can be combined to get new insights for research (e.g. drug development), hospital management (e.g. predictive analytics), public health, (e.g. simulation for health planning tasks) and patient empowerment.

ELIXIR, the research infrastructure for biological information is in charge of managing and safeguarding the massive amounts of data being generated in biological and life science research where BBMRI-ERIC, the research infrastructure for Biobanking and BioMolecular resources takes care of all sample and patient related information.  The cooperation between these two pan-European research infrastructures is described in a Memorandum of Understanding, and there are several common (H2020 funded) research projects connecting the 2 research communities.

A close cooperation, both on the European as on the national level, of BBMRI and ELIXIR will answer the following needs of the research community and stakeholders from public health, industry and patients organizations.

Feedback of research data to the clinics

Addition of data from clinical information systems to this research, and reverse feedback of research data into the clinic adds much more potential to rapidly develop new opportunities into research and clinical applications. However, this is beyond what most electronic patient records can facilitate today. New techniques produce huge amounts of data that cannot readily be interpreted by a medical professional. New analytics, new workflows and new visualizations are needed. Meanwhile, population-based methods are emerging from research further enabling data integration, visualization and prediction to unlock the full potential for medical decision making.

Integration of Public Health data

The integration of public data for disease modelling is also a key facilitator for future systems of medical applications and solutions. Deposition of published data in public databases is common practice these days in biomedical research.

New research and clinical applications require increasingly large cohorts & populations, high-resolution data and high quality samples. Data from next generation measurement techniques based on large biobank cohorts need to be increasingly connected to molecular and clinical data to facilitate the understanding and treatment of complex diseases, patient stratification for improved patient care and more precise diagnostics.

Patient Empowerment

What, if patient data is not under patient control? A paradox example of how user data is not accessible are health records. Even, when the legislation forces medical stakeholders to make records available to patients, but those aren’t particularly helpful when a patient is not informed about the existence of his data. And the situation is even more complex when we look at data gathered by (fitness) sensors and social networks. Formally, data owners are requested by the law to publish the relevant policy explaining how they protect users’ personal data, what they’ll do with that data and how to access and request information on personal data processing activities. In practice, it is not easy for users to track the processing of their personal data, to receive relevant information on such processing operation and to access their data. Clearly, Controlling and Accessing Patient Data Shouldn’t Just Be a Privilege. The data protection legislation is pushing for more transparency to enable the users to know what exactly a data controller and data processor collects, whether through a website, a physical device, or other means. That, in turn, makes the data owner/ data subject in a position to decide, supposing he is supported with the necessary information and software tools.

4.3 Benefits to Austria of membership of ELIXIR

There are many benefits to Austria of joining ELIXIR, most notably the opportunity of collaborating with and jointly developing a data infrastructure with the leading partners in Europe. Additionally, Members of ELIXIR also benefit from the following activities:

Participation in ELIXIR’s EU applications

ELIXIR is active in applying to EU funding. It has recently been awarded a large implementation grant from Horizon 2020. The ELIXIR-EXCELERATE project will kick off in September 2015. The contribution from the European Commission is EUR 19 million over 4 years, and this will be allocated to ELIXIR partner organisations in 16 countries. In addition, ELIXIR is also the coordinator of CORBEL, the new EUR 14.5 million ESFRI cluster project for the Bio Medical Science Research Infrastructures. This is co-coordinated by BBMRI.

ELIXIR was also active in other Horizon 2020 applications, and with much success. The table below shows the successful applications in the first round of Calls that were led by ELIXIR or in which ELIXIR was a partner.

H2020 Call          

Project

ELIXIR’s role

Total project budget

 

 

 

 

INFRADEV3

EXCELERATE

Led by ELIXIR Hub

€19,051,483

INFRADEV4

CORBEL

Led by ELIXIR Hub

€14,837,806

INFRADEV4

ENVRI PLUS

Partner

€14,998,038

INFRADEV4

EMBRIC

Partner

€9,041,612

E-INFRA-1-2004

EGI-ENGAGE

Partner

€8,668,754

Teaming

ARTEMIDA

Led by ELIXIR Slovenia

€499,833

As a priority research infrastructure for Europe, where there are numerous topics of relevance to bioinformatics in the Health Grand Challenge, Innovative Medicines Initiative, LEIT Biotechnology, and Research Infrastructure themes of H2020, the opportunity for the Austrian bioinformatics community to engage in Horizon 2020 through ELIXIR is immense.

Participation in Pilot Actions

ELIXIR funds Pilot Actions (www.elixir-europe.org/about/pilot-projects), which are funded by the ELIXIR Hub budget but carried out by the ELIXIR Nodes. Support through ELIXIR Pilot Actions are focused on countries that have signed the ECA - the budget for Pilot Actions in 2015 is around 10-20% of the Hub operating costs. In future, as technical activities ramp up and the staff costs in Hub remain stable, a larger proportion of the budget will go on such technical activities in the Nodes.

ELIXIR Commissioned services

We are currently developing plans for Commissioned Services, which are long-term investments in ELIXIR Nodes to run services for users. In many cases they will build on ELIXIR Pilots and follow the same principle of using ELIXIR Hub budget to support services run by ELIXIR Nodes.

ELIXIR Node development programme

ELIXIR’s Node development and capacity building programme will allow those countries that are in the process of developing their national bioinformatics infrastructure to adopt best practice from established national Nodes such as the SIB Swiss Institute of Bioinformatics. Support is provided to Nodes on aspects including establishing legal and governance models for the Node, using the Linked Third Party clause in Horizon 2020, developing business cases for national roadmap applications and accessing EU Structural Funds.

ELIXIR’s industry programme

ELIXIR Members can benefit from the ELIXIR Innovation and SME Programme (www.elixir-europe.org/industry/supporting-industry-users), where local events, funded by the ELIXIR Hub, are organised by and hosted in ELIXIR Nodes. Hosting an event in Austria could directly support national research-intensive companies and SMEs. Through local, hands-on training and showcasing of ELIXIR’s resources, the companies attending are able to integrate ELIXIR’s services into their own research and product development.