TY - GEN A1 - Becker, Pascal-Nicolas A1 - Bertelmann, Roland A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Heidrich, Regina A1 - Höhnow, Tobias A1 - Kassube, Michael A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Landes, Lilian A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schobert, Dagmar A1 - Schwab, Oliver A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Stoyanova, Tonka A1 - Vierkant, Paul T1 - DeepGreen – Metadata Schema for the exchange of publications between publishers and open access repositories. Version 1.1. June 2016 N2 - In 2011, important priorities were set to realize green publications in the open access movement in Germany. With financial support from the German Research Foundation (DFG), libraries negotiated Alliance licenses with publishers that guarantee extensive open access rights. Authors of institutions, that have therewith access to licensed journals, can freely publish their articles immediately or after a short embargo period in a repository of their choice. However, authors hesitantly use these open access rights. Also libraries – as managers of institutional and subject based repositories and thus legitimated representatives for the authors – only rarely make use of these rights. The aim of DeepGreen is to make the majority of those publications available online. Together with publishers of the Alliance licenses, the project consortium wants to develop a nearly fully automated workflow that covers both the delivery of data, including the full texts, of the publishers, as well as the data transformation to the necessary import formats and the loading process into the repositories. An intermediate “publication router” will serve as a distribution platform. The DeepGreen metadata schema contains metadata properties describing a wide range of deliverable bibliographic metadata from the Alliance license publishers (most common standards are JATS and CrossRef XML) as well as its compliance with technical, quality and metadata standards of the repositories. The schema includes required metadata elements and optional properties providing additional information.The metadata schema is aligned to the OCLC repository best practices (“Best Practices for CONTENTdm and other OAI-PMH compliant repositories: creating sharable metadata”, URL: http://www.oclc.org/content/dam/support/wcdigitalcollectiongateway/MetadataBestPractices.pdf). The current version of the schema is subject to changes as the functional requirements and workflow practices are evolving during the project experiences and prototype production. T3 - ZIB-Report - 16-32 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59580 SN - 1438-0064 N1 - This work is in the public domain: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. https://creativecommons.org/publicdomain/zero/1.0/ ER - TY - GEN A1 - Behrens, Kathrin A1 - Bertelmann, Roland A1 - Boltze, Julia A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Hammerl, Michaela A1 - Haoua, Marsa A1 - Heermann, Petra A1 - Hoffmann, Cornelia A1 - Höhnow, Tobias A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Staub, Hedda A1 - Wannick, Eike T1 - DeepGreen - Open Access Transformation: Eine Handreichung für institutionelle Repositorien BT - Version 1.0 N2 - Mit dem DFG-geförderten Projekt DeepGreen soll eine automatisierte, rechtssichere Lösung entwickelt werden, um Artikeldaten von wissenschaftlichen Verlagen abzuholen und anschließend, nach Ablauf etwaiger lizenzrechtlicher Embargofristen, an berechtigte Repositorien zu verteilen und somit in den Open Access zu überführen. Dabei liegt der Fokus auf den DFG-geförderten und überregional verhandelten Allianz-Lizenzen, mit spezieller Open-Access-Komponente. Die vorliegende Handreichung richtet sich speziell an die Betreiber institutioneller Repositorien und stellt Empfehlungen und einen Workflow bereit, um eine erfolgreiche Veröffentlichung, der durch die DeepGreen-Datendrehscheibe zugeordneten Artikel, zu ermöglichen. Die Handreichung basiert auf den bisherigen Erfahrungen der DeepGreen-Projektbeteiligten. T3 - ZIB-Report - 19-31 KW - Open Access KW - Open-Access-Transformation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74438 SN - 1438-0064 ER - TY - GEN A1 - Becker, Pascal-Nicolas A1 - Bertelmann, Roland A1 - Ceynowa, Klaus A1 - Christof, Jürgen A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groß, Matthias A1 - Heidrich, Regina A1 - Höhnow, Tobias A1 - Kassube, Michael A1 - Koch, Thorsten A1 - Kuberek, Monika A1 - Landes, Lilian A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Schobert, Dagmar A1 - Schwab, Oliver A1 - Schwidder, Jens A1 - Söllner, Konstanze A1 - Stoyanova, Tonka A1 - Vierkant, Paul T1 - Questionnaire for effective exchange of bibliographic metadata – current status of publishing houses N2 - The project DeepGreen aims to realise better usage of green open access publication rights with regard to Alliance Licenses in Germany (https://www.nationallizenzen.de/open-access). Together with publishers who offer Alliance Licenses and authorized libraries, the project group intends to develop a prototype of a nearly fully automated workflow that covers the delivery of data from the publishers, including the article full texts, as well as the process of loading data into the institutional repositories of licensees. Further information about the project can be found within ZIB-Report 15-58, urn:nbn:de:0297-zib-56799. In order to become acquainted with publishers’ processes for exchanging documents and metadata, the project group developed a questionnaire for an online survey. The publishing of this questionnaire is intended to demonstrate relevant aspects of the issue (e. g. methods of data exchange, protocols and interfaces) and to foster reuse of valuable questionnaire elements. The XML-file can be reused as a template, the PDF-file reproduces the original survey layout. KW - Open Access KW - Open Access KW - Questionnaire Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60419 N1 - This work is in the public domain: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. https://creativecommons.org/publicdomain/zero/1.0/ ER - TY - GEN A1 - Rusch, Beate A1 - Bertelmann, Roland A1 - Pampel, Heinz A1 - Aust, Pamela A1 - Helbig, Kerstin A1 - Müller, Anja Doreen A1 - Conrad-Rempel, Steffi A1 - Weihe, Signe A1 - Dierkes, Thomas A1 - Kuhlen, Rainer A1 - Schobert, Dagmar A1 - Voigt, Michaela A1 - Klimpel, Paul A1 - Riesenweber, Christina A1 - Kennecke, Andreas A1 - Kowalak, Mario A1 - Schlegel, Birgit A1 - Taubert, Niels A1 - Hübner, Andreas A1 - Mruck, Katja T1 - KOBV-Sonderedition zur International Open Access Week 2016 „Open in Action“ N2 - An der internationalen Open-Access-Woche 2016 vom 24.-28. Oktober war der KOBV erstmalig mit einem Online „Publishing Event“ beteiligt. An fünf aufeinanderfolgenden Tagen erschien täglich eine Sonderausgabe des KOBV-Newsletters zu ausgewählten Open-Access-Themen. Die einzelnen Beiträge sind in dieser Sonderedition als Online-Reader zusammengestellt. Der aktuelle Diskussionsstand zum jeweiligen Thema wird von Expertinnen und Experten in kurzen Übersichtsartikeln vorgestellt und mit Praxistipps ergänzt. Zielgruppe sind vor allem Bibliothekare und Bibliothekarinnen, die sich einen schnellen Überblick zu Open Access verschaffen wollen. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60708 ER - TY - GEN A1 - Ehrig, Rainald A1 - Dierkes, Thomas A1 - Schäfer, Stefan A1 - Röblitz, Susanna A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Alimguzhin, Vadim A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian A1 - Leeners, Brigitte T1 - An Integrative Approach for Model Driven Computation of Treatments in Reproductive Medicine N2 - We present an overview of the current status of the European collaborative project PAEON. The challenge of PAEON is to provide specialists in reproduc- tive medicine with a computerised model of the menstrual cycle under normal and various pathological conditions, which will allow them to get further in- sight in fertility dynamics. This model also enables the simulation of treatment protocols, which were used within in vitro fertilization. By the definition of virtual patients through biologically admissible parametrizations our approach allows not only the evaluation of a given treatment strategy in silico, but also the design and optimization of such protocols. Once a protocol is formalized in the virtual hospital, the success can be controlled by a treatment execution monitor, which works then as a clinical decision support system. All these tools will be combined in a virtual hospital environment, enabling the access to the PAEON services through the web. T3 - ZIB-Report - 16-04 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57103 SN - 1438-0064 ER - TY - GEN A1 - Dierkes, Thomas T1 - Construction of ODE systems from time series data by a highly flexible modelling approach N2 - In this paper, a down-to-earth approach to purely data-based modelling of unknown dynamical systems is presented. Starting from a classical, explicit ODE formulation y=f(t,y) of a dynamical system, a method determining the unknown right-hand side f(t,y) from some trajectory data y_k(t_j), possibly very sparse, is given. As illustrative examples, a semi-standard predator-prey model is reconstructed from a data set describing the population numbers of hares and lynxes over a period of twenty years [1], and a simple damped pendulum system with a highly non-linear right-hand side is recovered from some artificial but very sparse data [2]. T3 - ZIB-Report - 15-59 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56768 SN - 1438-0064 ER - TY - JOUR A1 - Dierkes, Thomas T1 - Construction of ODE systems from time series data by a highly flexible modelling approach JF - ArXiv e-prints N2 - In this paper, a down-to-earth approach to purely data-based modelling of unknown dynamical systems is presented. Starting from a classical, explicit ODE formulation y=f(t,y) of a dynamical system, a method determining the unknown right-hand side f(t,y) from some trajectory data y_k(t_j), possibly very sparse, is given. As illustrative examples, a semi-standard predator-prey model is reconstructed from a data set describing the population numbers of hares and lynxes over a period of twenty years, and a simple damped pendulum system with a highly non-linear right-hand side is recovered from some artificial but very sparse data. Y1 - 2015 VL - math.NA 1512.03357 ER - TY - JOUR A1 - Dierkes, Thomas T1 - Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert? JF - ABI Technik N2 - Thomas Dierkes ist promovierter Mathematiker und als Entwickler beim Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) am Zuse-Institut Berlin (ZIB) tätig. Er arbeitet dort an der Entwicklung einer „Datendrehscheibe“ für die Umsetzung der Open-Access-Komponente in Allianz-Lizenzen. Er beantwortet die aktuelle Abi Technikfrage: „Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert?“ Y1 - 2017 U6 - https://doi.org/10.1515/abitech-2017-0051 VL - 37 IS - 3 SP - 237 ER - TY - CHAP A1 - Ehrig, Rainald A1 - Dierkes, Thomas A1 - Schäfer, Stefan A1 - Röblitz, Susanna A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Alimguzhin, Vadim A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian A1 - Leeners, Brigitte T1 - An integrative approach for model driven computation of treatments in reproductive medicine T2 - BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India Y1 - 2016 ER - TY - JOUR A1 - Rusch, Beate A1 - Boltze, Julia A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Staub, Hedda T1 - DeepGreen - DeepGold: Open-Access-Transformation - Entwicklung und Perspektiven JF - GMS Medizin - Bibliothek - Information N2 - Das deutsche Projekt DeepGreen (https://deepgreen.kobv.de/de/deepgreen/) arbeitet an einer automatisierten Lösung, um Artikeldaten (Volltexte und Metadaten) von wissenschaftlichen Verlagen abzuholen und an Repositorien zu liefern, die diese Artikel wiederum Open Access veröffentlichen können. Ausgangspunkt für das Projekt sind die überregional geförderten deutschen Allianz-Lizenzen. Diese enthalten eine Open-Access-Komponente, die es Autor*innen oder deren Institution erlaubt, ihre Artikel nach einer verkürzten Embargofrist in einem Repositorium ihrer Wahl Open Access zugänglich zu machen. DeepGreen wird seit 2016 von der Deutschen Forschungsgemeinschaft gefördert (1. Förderphase: 01.2016–12.2017; 2. Förderphase: 08.2018–07.2020) und besteht aus einem Konsortium aus 6 Institutionen: Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV), Bayerische Staatsbibliothek (BSB), Bibliotheksverbund Bayern (BVB), Universitätsbibliothek der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum Potsdam (GFZ), Universitätsbibliothek der Technischen Universität Berlin (TUBB). Y1 - 2019 U6 - https://doi.org/10.3205/mbi000432 VL - 19 IS - 1-2 ER - TY - GEN A1 - Dierkes, Thomas A1 - Wade, Moritz A1 - Nowak, Ulrich A1 - Röblitz, Susanna T1 - BioPARKIN - Biology-related Parameter Identification in Large Kinetic Networks N2 - Modelling, parameter identification, and simulation play an important rôle in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years. T3 - ZIB-Report - 11-15 KW - systems biology KW - ordinary differential equations KW - sensitivity analysis KW - parameter identification KW - affine invariant Gauss-Newton algorithm KW - numerical library KW - graphical user interface Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-12706 ER - TY - CHAP A1 - Mancini, Toni A1 - Salvo, Ivano A1 - Mari, Federico A1 - Melatti, Igor A1 - Massini, Annalisa A1 - Sinisi, Stefano A1 - Tronci, Enrico A1 - Davi, Francesco A1 - Dierkes, Thomas A1 - Ehrig, Rainald A1 - Röblitz, Susanna A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Egli, Marcel A1 - Ille, Fabian T1 - Patient-Specific Models from Inter-Patient Biological Models and Clinical Records T2 - Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014) Y1 - 2014 SP - 207 EP - 214 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Röblitz, Susanna A1 - Wade, Moritz A1 - Deuflhard, Peter T1 - Parameter identification in large kinetic networks with BioPARKIN JF - CoRR - Computing Research Repository - arXiv.org Y1 - 2013 UR - arxiv.org/abs/1303.4928v2 VL - abs/1303.4928 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Ortmann, Karl Michael T1 - On the efficient utilisation of duration JF - Insurance: Mathematics and Economics N2 - In this article we present a new approach to estimate the change of the present value of a given cashflow pattern caused by an interest rate shift. Our approximation is based on analysing the evolution of the present value function through a linear differential equation. The outcome is far more accurate than the standard approach achieved by a Taylor expansion. Furthermore, we derive an approximation formula of second order that produces nearly accurate results. In particular, we prove that our method is superior to any known alternative approximation formula based on duration. In order to demonstrate the power of this improved approximation we apply it to coupon bonds, level annuities, and level perpetuities. We finally generalise the approach to a non-flat term structure. As for applications in insurance, we estimate the change of the discounted value of future liabilities due to a proportional shift in the set of capital accumulation factors. These findings are of particular importance to capital adequacy calculations with respect to interest rate stress scenarios that are part of regulatory solvency requirements. Y1 - 2015 U6 - https://doi.org/10.1016/j.insmatheco.2014.11.002 VL - 60 SP - 29 EP - 37 ER -