Tomislav Cernava (Graz University of Technology, Institute of Environmental Biotechnology)
I am an assistant professor at the Graz University of Technology in the institute of Environmental Biotechnology. Our scientific work is mainly focused on the fields of Microbiome Research, Plant Protection and Bioprospecting. To drive this research areas we employ established micro- and molecular biology techniques as well as new omics technologies. With our scientific efforts we are developing new strategies and applications for biotechnological products.
We’re also very collaborative and have various projects with other teams, where efficient and secure data sharing becomes essential for us. Therefore, I joined the CyVerse Austria workshop, to become more familiar with data management and sharing on CyVerse, as well as shared analysis using Docker technology.
Clemens Diwoky (University of Graz, Institute of Molecular Biosciences)
I am a staff scientist in the core facility for preclinical MRI at the Karl-Franzens University of Graz. In my research I use preclinical in vivo imaging to investigate a variety of biological research questions such as lipases and their role in lipid associated disorders, polyamines in aging and disease and peptide-based cancer treatment.
Preclinical in vivo imaging is an important step in the evaluation process of biological hypotheses in health and disease of higher organisms (mainly small mammals). Its value is based in the acquisition of quantitative and qualitative (image based evidence) biomarkers in vivo. Allowing longitudinal investigations within a subject (e.g. a mouse) through its non-invasive character makes it one of the most powerful tools to take a deep look into physiologic function, structure and organ development in vivo.
I think CyVerse Austria can be a very useful tool to support my research. Every acquired imaging dataset is part of an animal experiment. Therefore every image is of high value in the sense of ethics and from a financial point of view. MRI acquisitions come along with a huge amount of Metadata. They mainly describe and parametrize the performed image acquisition and post processing steps. Documentation of those steps together with archiving raw data together with the corresponding resultant images, applied segmentations and the quantitative results would be an application I am thinking of.
Therefore different layers of CyVerse might be of interest for me, starting from data storage and management, metadata handling, but also linking existing image processing scripts to CyVerse.
Florian Ph.S Fischmeister (University of Graz, Institute of Psychology)
I am a senior PostDoc in neuropsychology and neuroimaging at Karl-Franzens University of Graz and at the Medical University of Vienna. In my research, I try to investigate key concepts of our brain “How does the brain work? How do we think?” In order to do that, I use an interdisciplinary approach by combining fMRI data with behavioural studies as well as microbiome data. We investigate, among others, neuroplasticity as well as longitudinal changes in patients. We’re therefore working in the big data field and have an urgent need for proper research data management and reproducible analysis.
I participated in the CyVerse workshop to get to know a platform which combines research data management with an analytical layer for re-usable and reproducible research.
Christoph Hahn (University of Graz, Institute of Biology)
I am an Assistant Professor at the Institute of Biology, University of Graz and an evolutionary biologist interested in the evolution and the genomic bases of ecological and behavioural adaptive traits in a range of study systems including parasitic flatworms and cichlid fishes. I use a variety of different technologies for my research, starting from de novo genome assembly, comparative genomics, methylomics, phylogenomics, population genomics, and general bioinformatics pipeline development (reconstruction of organellar genomes, eDNA metabarcoding data analysis). In my research, I highly encourage my team to use open science practices and I am keen on ensuring reproducibility of my analyses.
I joined the CyVerse workshop to learn more about the potential of the platform with regards to workflow implementation and connection with HPC clusters. In addition, in my opinion the implementation of Jupyter notebooks in CyVerse Austria is a very interesting option, also for teaching activities.
Michael Hetmann (University of Graz, Institute of Molecular Biosciences)
I am a PhD student in the structural biology group at the Institute of Molecular Biosciences at Karl-Franzens University of Graz. The focus of my research are enzymes and what is key for their catalytic ability. To study this I employ structural bioinformatics methods like molecular dynamic simulations or molecular docking. In addition to that I use different protein expression systems to obtain recombinant proteins, which are then further investigated using different biophysical methods. I am part of a project, which focuses on the family of BBE-like proteins. These proteins occur in plants, fungi and bacteria and for most of them their physiological function is unknown. As part of my project, I aim at functionally annotating these BBE-like proteins. I attended the CyVerse workshop to learn more about data management in order to be able to manage the data I generate during my PhD studies in a reproducible and re-usable way and share it with collaborators. Furthermore, people in my group are already working with the docker technology and therefore, CyVerse might be an attractive solution to share our tools.
Eduardo Machado-Charry (Graz University of Technology, Institute of Solid-State Physics)
I am a senior researcher at the Institute of Solid-State Physics at Graz University of Technology. I have a long experience developing, implementing, and applying numerical methods for different disciplines ranging from biophysics to material sciences. Currently, I am involved in a project with a consortium of 13 institutes at Graz University of Technology (TUG), University of Graz (KFUG), and Medical University of Graz (MUG) called Graz-µCT. This consortium will purchase an X-ray micro-computed tomography (µCT) infrastructure, which will be hosted at my Institute. Users from a wide variety of disciplines will use the infrastructure for their research; thus, we will generate large amounts of data. A typical user of a µCT device can collect terabytes of data in a single week. This data must be managed, documented, shared, and processed appropriately in our project to ensure re-usability and reliability of research data. We therefore aim at introducing well-structured research data management processes throughout the lifecycle of the data. CyVerse Austria (CAT) is already deployed at the three participating universities and, therefore, will serve as the tool of choice for our data management. CAT will help us to easily transfer the data from TUG, where the data is generated, to the partners at MUG and KFUG. Besides, through metadata schema in CAT and laboratory notebooks Powered by CAT, we will ensure adequate documentation. Finally, we aim to implement our data processing tools as Docker images in CAT to cover the whole data workflow on one platform.
Alexander Mahnert (Medical University of Graz, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine)
I am a postdoctoral researcher at the Medical University of Graz in the group of interactive microbiome research. We are using a variety of different techniques such as NGS, metabolite profiling, FISH, antibody or FACS based cell sorting as well as adapted cultivation strategies in order to do microbiome studies in various habitats. One research focus in our team are human-associated archaea and the microbiome of confined built environments like hospitals. Furthermore, we are interested in stabilizing or manipulating beneficial microbial diversity in indoor environments and the human host. Within these endeavors, we are collaborating with researchers at the Technical University of Graz. Since we are a Medical University, we also work with sensitive patient data. and also have special requirements regarding data safety. Therefore, CyVerse Austria is a safe solution for our data sharing needs in such collaborative projects.
Gustav Oberdorfer (Graz University of Technology, Institute of Biochemistry)
I am a university assistant at the Institute of Biochemistry of the Graz University of Technology. My research focuses on computational protein design. Such designed proteins can be further used as building blocks for higher complexity structures and biomaterials. With my recently acquired funding (ERC starting grant, FWF standalone, ERC FET-Open) I was able to start my own research team at TU Graz. In all of these projects, my team members and I computationally design de novo proteins and experimental characterize them.
Besides other techniques, we use the macromolecular modelling software Rosetta for ab initio protein structure prediction. I joined the CyVerse workshop in order to make these tools easy-to-use for my students and to ensure reproducible research.
Manfred Sagmeister (Medical University of Graz, Division of General Paediatrics)
I am a research associate at the Medical University of Graz at the Department of general pediatrics. In my research I focus on alterations of the host genome in patients affected by various diseases by performing genome-wide association studies (GWAS). The support of international cooperation partners help me in the acquisition of genotype data from various populations used for case/control studies. In those projects I do all the steps from raw data preparation until final analysis. Therefore, CyVerse Austria would be a powerful tool for me in order to implement data management steps for those big data studies. In addition, in the international context it would be great to use CyVerse to ensure reproducible analysis using Docker technologies but by avoid transferring sensitive data to other countries.
Gerhard Thallinger (Graz University of Technology, Institute of Computational Biotechnology)
I am principal investigator at the Institute of Computational Biotechnology, Graz University of Technology. Research in my team covers management and processing of high-throughput screening data as well as the development of databases and tools for their computational analysis. Specifically we are interested in the analysis of diverse dataset generated with next generation sequencing technologies and mass spectrometry and the integration of multiple omics datasets in a joint evaluation. Recent projects in my team include screening for new enzymes for polymer modification, comparative phylogeography of co-distributed arboreal mites or tumour therapy selection based on molecular.
I joined the CyVerse workshop because I am very keen on using open science practices in my daily research and I am very enthusiastic about FAIR data management and reproducibility. Since we are working with huge data amounts and diverse software tools with different versions, I am sure that a platform such as CyVerse will help to overcome current hurdles in the bioinformatics field and will help to improve the reproducibility of data analyses in biomedical research.
Slave Trajanoski (Medical University of Graz, Core Facility Computational Bioanalytics)
I am at the Center for medical research working in the CF Computational Bioanalytics. In this position, I interact with a variety of researchers at the Medical University Graz and help them with their analytical infrastructure needs.
We provide different tools for them (e.g. Galaxy galaxy.medunigraz.at) to analyze their research data and with CyVerse Austria we also have a powerful and robust platform for data sharing, which is a sensitive topic within the medical university.
I am also involved in the user support for Cyverse Austria in order to help users to efficiently make use of the platform for data management and sharing, as well as data analytics. I joined the CyVerse workshop to get more familiar with Docker technologies and their implementation in CyVerse Austria.
Mojib Wali (Graz University of Technology, Institute of Interactive Systems and Data Science)
I am a software developer at TU Graz in the Open and Reproducible Research group. In our team, we’re focussing on Open Science and develop tools and services for researchers to make their data FAIR and their research reproducible.
More precisely, I am involved in the development of InvenioRDM. This open-source is being developed as part of a large, multi-organization collaboration in partnership with CERN. Together we are working to build a turnkey open-source research data management platform to support data sharing, innovation, knowledge dissemination, and interdisciplinary collaboration.
I participated in the workshop, because CyVerse Austria supports the preceding step of the research data lifecycle before final archival (e.g. in InvenioRDM). Therefore, a cross-talk between those two systems would be an interesting approach for TUG researchers.
Heimo Wolinski (University of Graz, Institute of Molecular Biosciences)
I am senior scientist at the Institute of Molecular Biosciences of the University of Graz. My research mainly focuses on lipid metabolism, especially (de-)regulation of lipid droplets and fat tissue. I am particularly interested in studying the mechanisms causing lipodystrophies. These are genetic or acquired human disorders characterized by a complete or partial lack of body fat. The absence of fat tissue is associated with metabolic complications such as insulin resistance, hypertriglyceridemia or fatty liver. Genetic lipodystrophies are unhealable. For my studies I am using molecular and cell biological techniques including high-end optical imaging an advanced image processing approaches. In addition, I am the head of the Microscopy Core Facility of the Institute. I attended the CyVerse workshop in order to get to know a new tool implemented into CyVerse for data management with a particular focus on imaging data. Not least due to the data management requirements from our main funding agencies, we as researchers, really need those solutions.
Florian Wieser (Graz University of Technology, Institute of Biochemistry)
I recently started my PhD studies at Graz University of Technology at the Institute of Biochemistry in the team of Gustav Oberdorfer. In my project I will make use of the structure prediction tool Rosetta in order to screen a variety of different proteins for their three-dimensional structures. Additionally, I will attempt to further extend the functionality of Rosetta.
I joined the CyVerse workshop to learn about efficient data management practices for my PhD studies and I’d like to implement specific tasks of Rosetta as a tool in CyVerse in order to ensure an easy-to-use interface for the tool.