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Curation at GFBio Data Centers

Tanja Weibulat, Maren Gleisberg, Birgit Klasen, Ivaylo Kostadinov, Jimena Linares, Anke Penzlin, Judith Weber
2021 Zenodo  
Poster GFBio-10 from the GFBio General Assembly 2021 of the GFBio Project summarizing the projects and subtasks work and outcome between 2013 and 2021. The ten GFBio Data Centers act as infrastructure partners in the GFBio broker network. Data submitted to GFBio are trans- mitted to and curated by data curators at the GFBio Data Centers. The submitted data are enriched with metadata, dependent on the data type, data format and data content. This is done in close collaboration with the data producer.
doi:10.5281/zenodo.5793975 fatcat:zibmqa7cqje3tcx5yqeqcwzz6a

Practical MANETs for Pervasive Cattle Monitoring

Bartosz Wietrzyk, Milena Radenkovic, Ivaylo Kostadinov
2008 Seventh International Conference on Networking (icn 2008)  
The application of Mobile Ad Hoc Networks to cattle monitoring has the potential to increase the profitability of cattle production and positively impact the everyday live of farm personnel. The main research challenges are identifying and refining realistic requirements for a MANET routing protocol and designing such protocol. In this paper we report on the field experiments we performed in order to address this. Our approach builds on energy efficient MANETs to provide continuous monitoring
more » ... multidimensional parameters of animal mobility including temporal and spatial walking intensity and feed intake in order to detect oestrus, pregnancy, animal diseases and reduced efficiency of pastures. We support remote and in-situ, specific and range queries and notifications about newly detected events. Our extensive set of emulations show that we achieve lower and more balanced energy consumption while preserving the delays for increasing number of nodes within the user expected boundaries. Seventh International Conference on Networking 978-0-7695-3106-9/08 $25.00
doi:10.1109/icn.2008.78 dblp:conf/icn/WietrzykRK08 fatcat:bkxfdtmkarbbrfmtqhrbgiwcyy

NFDI4BioDiversity - NFDI-Konsortium für Biodiversitäts-, Ökologische und Umweltdaten

Judith Weber, Barbara Ebert, Michael Diepenbroek, Ivaylo Kostadinov, Frank Oliver Glöckner
2021 Bausteine Forschungsdatenmanagement  
., Kostadinov, I., Yahyapour, R., Müller, W. Scholz, U., Triebel, D., Frenzel, M., Gemeinholzer, B., Goesmann, A., König-Ries, B., Bonn, A., Seeger, B. (2020, July 14).  ...  11 https://www.gbif.org, abgerufen am 29.01.2021. 12 https://www.coretrustseal.org, abgerufen am 29.01.2021. cb Für eine detaillierte Beschreibung der GFBio Services siehe Astor, T., Weber, J., Kostadinov  ... 
doi:10.17192/bfdm.2021.2.8334 fatcat:npxhouevkngvlmxlkpqd44kgxe

CORBEL Ocean Sampling Day: a demonstrator of a cross-domain distributed data set

Frank Oliver Glöckner, Ivaylo Kostadinov, Guy Cochrane
2020 Zenodo  
This work addresses the establishment of cross-domain data sets as exemplified by the Ocean Sampling Day. To fulfil this goal a workflow based on the broker service of GFBio to concurrently submit molecular (sequence) data and environmental data to ENA and PANGAEA, by conserving the dependency of the two datasets. With this standard compliant workflow, incremental submissions of large-scale datasets can be easily handled and sustainable cross-linking between two internationally known, long-term repositories were established.
doi:10.5281/zenodo.3839956 fatcat:xkioh5rkn5cbhfa2pbbzkjqrfy

Increasing communication reliability in manufacturing environments

Milena Radenkovic, Ivaylo Kostadinov, Bartosz Wietrzyk
2015 2015 International Wireless Communications and Mobile Computing Conference (IWCMC)  
This paper is concerned with low cost mechanisms that can increase reliability of machine to machine and machine to cloud communications in increasingly complex manufacturing environments that can be disconnection and fault prone. We explore a distributed and cooperative sensing framework that supports localized real time predictive analytics of connectivity patterns and detection of a range of faults together with issuing of notifications and responding on demand queries. We show that our
more » ... and Disconnection Aware Smart Sensing (FDASS) framework achieves significantly higher packet delivery ratios and lower communication delays in the face nodes and network unreliability when compared to the state of art and benchmark approaches.
doi:10.1109/iwcmc.2015.7289283 dblp:conf/iwcmc/RadenkovicKW15 fatcat:zqb4ddvab5egjfaqfuntslaa6i

FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives [article]

Christiane Hassenrueck, Tobias Poprick, Veronique Helfer, Massimiliano Molari, Raissa Meyer, Ivaylo Kostadinov
2021 bioRxiv   pre-print
Knowledge derived from nucleotide sequence data is increasing in importance in the life sciences, as well as decision making (mainly in biodiversity policy). Metadata standards have been established to facilitate sustainable sequence data management according to the FAIR principles (Findability, Accessibility, Interoperability, Reusability). Here, we review the status of metadata available for raw read Illumina amplicon and whole genome shotgun sequencing data derived from ecological
more » ... material that are accessible at the European Nucleotide Archive (ENA), as well as the compliance of the primary sequence data (fastq files) with data submission requirements. While overall basic metadata, such as geographic coordinates, were retrievable in 98% of the cases for this type of sequence data, interoperability was not always ensured and other (mainly conditionally) mandatory parameters were often not provided at all. Metadata standards, such as the 'Minimum Information about any(x) Sequence (MIxS)', were only infrequently used despite a demonstrated positive impact on metadata quality. Furthermore, the sequence data itself did not meet the prescribed requirements in 31 out of 39 studies that were manually inspected. To tackle the most immediate needs to improve FAIR sequence data management, we provide a list of minimal suggestions to researchers, research institutions, funding agencies, reviewers, publishers, and databases, that we believe might have a potentially large positive impact on sequence data and metadata FAIRness, which is crucial for further research and its derived applications.
doi:10.1101/2021.09.23.461561 fatcat:wqk6tuw4gfhkpfjqvl6lory5fu

Potential für ein starkes Netzwerk zwischen GFBio und FDM-Beratenden an Universitäten und Forschungsinstituten

Tina Astor, Judith Weber, Ivaylo Kostadinov, Frank Oliver Glöckner, Jens Nieschulze
2021 Bausteine Forschungsdatenmanagement  
, Ivaylo, Nieschulze, Jens, Seeger, Bernhard, Tolksdorf, Robert & Triebel, Dagmar, "Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: The German Federation  ...  Datenabgabe unterstützen, wenn es bei- spielsweise im 7 Datenzugang 8 9 Fazit Diepenbroek, Michael, Glöckner, Frank Oliver, Grobe, Peter, Güntsch, Anton, Huber, Robert, König-Ries, Birgitta, Kostadinov  ... 
doi:10.17192/bfdm.2021.1.8311 fatcat:6gtdgyoe2fh77b4u5pkvjtuuxa

iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists [article]

Miguel Vences, Aurelien Miralles, Sophie Brouillet, Jacques Ducasse, Alexander Fedosov, Vladimir Kharchev, Ivaylo Kostadinov, Sangeeta Kumari, Stefanos Patmanidis, Mark D Scherz, Nicolas Puillandre, Susanne S. Renner
2021 bioRxiv   pre-print
While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and
more » ... centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The alpha version (iTaxoTools 0.1) distributed with this paper contains GUI versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses.
doi:10.1101/2021.03.26.435825 fatcat:52zzf5thi5chbo52lqcjruph2q

iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

MIGUEL VENCES, AURÉLIEN MIRALLES, SOPHIE BROUILLET, JACQUES DUCASSE, ALEXANDER FEDOSOV, VLADIMIR KHARCHEV, IVAYLO KOSTADINOV, SANGEETA KUMARI, STEFANOS PATMANIDIS, MARK D. SCHERZ, NICOLAS PUILLANDRE, SUSANNE S. RENNER
2021 Megataxa  
While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and
more » ... ntered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)
doi:10.11646/megataxa.6.2.1 fatcat:mtae5o6uargtdjtvgwapn55jqi

Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes

Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg, Frank Glöckner
2011 Microbial Informatics and Experimentation  
The list of 53 HMMs was based on Ciccarelli et al. 2006 (Additional file 1, Kostadinov et al.  ... 
doi:10.1186/2042-5783-1-9 pmid:22587903 pmcid:PMC3372289 fatcat:jwza6fxecrdezgeelmo5bl5phm

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Duhaime, Jörg Peplies, Frank Glöckner
2008 BMC Bioinformatics  
Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.
more » ... : The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion: JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.
doi:10.1186/1471-2105-9-177 pmid:18380896 pmcid:PMC2311307 fatcat:vbdqmtjs6nceril6d4snhltvre

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

Pier Luigi Buttigieg, Wolfgang Hankeln, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, Frank Oliver Glöckner, Iddo Friedberg
2013 PLoS ONE  
The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems
more » ... accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings: We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to wellsupported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious "guilty-by-association" approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance: Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.
doi:10.1371/journal.pone.0050869 pmid:23516388 pmcid:PMC3597751 fatcat:aaj3ypng3fb6dbcrg62tmsfo2a

CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data

Wolfgang Hankeln, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner, Sarah K. Highlander
2011 PLoS ONE  
State of the art (DNA) sequencing methods applied in "Omics" studies grant insight into the 'blueprints' of organisms from all domains of life. Sequencing is carried out around the globe and the data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental data, as well as information about the environment are rarely submitted along with the sequence
more » ... a. If these contextual or metadata are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. In a recent community effort the GSC has developed a series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific community to significantly enhance the quality and quantity of contextual data in the public sequence data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate contextual and sequence data in (Multi)FASTA format prior to submission.
doi:10.1371/journal.pone.0024797 pmid:21935468 pmcid:PMC3172294 fatcat:brnhmajpufckvetzw3zg5rckbe

NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI)

Frank Oliver Glöckner, Michael Diepenbroek, Janine Felden, Anton Güntsch, Jens Stoye, Jörg Overmann, Klaus Wimmers, Ivaylo Kostadinov, Ramin Yahyapour, Wolfgang Müller, Uwe Scholz, Dagmar Triebel (+6 others)
2020 Zenodo  
Ivaylo Kostadinov GFBio e.V., Bremen TA 5 Prof. Dr. Ramin Yahyapour GWDG, Göttingen TA 2 Dr. Wolfgang Müller HITS, Heidelberg TA 4 Dr. Uwe Scholz IPK, Gatersleben TA 4 Dr.  ...  Sustainability and business model Frank Oliver Glöckner (UniBremen-MARUM) Ivalyo Kostadinov (GFBio e.V.)  ... 
doi:10.5281/zenodo.3943644 fatcat:lltfs5w6y5hn3ixe5bw2sitoa4

Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes

Dagmar Woebken, Hanno Teeling, Patricia Wecker, Alexandra Dumitriu, Ivaylo Kostadinov, Edward F DeLong, Rudolf Amann, Frank O Glöckner
2007 The ISME Journal  
Planctomycetes are widely distributed in marine environments, where they supposedly play a role in carbon recycling. To deepen our understanding about the ecology of this sparsely studied phylum six planctomycete fosmids from two marine upwelling systems were investigated and compared with all available planctomycete genomic sequences including the as yet unpublished nearcomplete genomes of Blastopirellula marina DSM 3645 T and Planctomyces maris DSM 8797 T . High numbers of sulfatase genes
more » ... 109) were found on all marine planctomycete genomes and on two fosmids (2). Furthermore, C1 metabolism genes otherwise only known from methanogenic Archaea and methylotrophic Proteobacteria were found on two fosmids and all planctomycete genomes, except for 'Candidatus Kuenenia stuttgartiensis'. Codon usage analysis indicated high expression levels for some of these genes. In addition, novel large families of planctomycete-specific paralogs with as yet unknown functions were identified, which are notably absent from the genome of 'Candidatus Kuenenia stuttgartiensis'. The high numbers of sulfatases in marine planctomycetes characterizes them as specialists for the initial breakdown of sulfatated heteropolysaccharides and indicate their importance for recycling carbon from these compounds. The almost ubiquitous presence of C1 metabolism genes among Planctomycetes together with codon usage analysis and information from the genomes suggest a general importance of these genes for Planctomycetes other than formaldehyde detoxification. The notable absence of these genes in Candidatus K. stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes.
doi:10.1038/ismej.2007.63 pmid:18043661 fatcat:c3yovn3r45cffo7rt47wi3kofe
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