@misc{BeckerBertelmannCeynowaetal., author = {Becker, Pascal-Nicolas and Bertelmann, Roland and Ceynowa, Klaus and Christof, J{\"u}rgen and Dierkes, Thomas and Goltz-Fellgiebel, Julia Alexandra and Groß, Matthias and Heidrich, Regina and H{\"o}hnow, Tobias and Kassube, Michael and Koch, Thorsten and Kuberek, Monika and Landes, Lilian and Pampel, Heinz and Putnings, Markus and Rusch, Beate and Sch{\"a}ffler, Hildegard and Schobert, Dagmar and Schwab, Oliver and Schwidder, Jens and S{\"o}llner, Konstanze and Stoyanova, Tonka and Vierkant, Paul}, title = {DeepGreen - Metadata Schema for the exchange of publications between publishers and open access repositories. Version 1.1. June 2016}, issn = {1438-0064}, doi = {10.12752/3.dg.1.0}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59580}, abstract = {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.}, language = {en} } @misc{BeckerBertelmannCeynowaetal., author = {Becker, Pascal-Nicolas and Bertelmann, Roland and Ceynowa, Klaus and Christof, J{\"u}rgen and Dierkes, Thomas and Goltz-Fellgiebel, Julia Alexandra and Groß, Matthias and Heidrich, Regina and H{\"o}hnow, Tobias and Kassube, Michael and Koch, Thorsten and Kuberek, Monika and Landes, Lilian and Pampel, Heinz and Putnings, Markus and Rusch, Beate and Sch{\"a}ffler, Hildegard and Schobert, Dagmar and Schwab, Oliver and Schwidder, Jens and S{\"o}llner, Konstanze and Stoyanova, Tonka and Vierkant, Paul}, title = {Questionnaire for effective exchange of bibliographic metadata - current status of publishing houses}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60419}, abstract = {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.}, subject = {Open Access}, language = {en} } @misc{EhrigDierkesSchaeferetal., author = {Ehrig, Rainald and Dierkes, Thomas and Sch{\"a}fer, Stefan and R{\"o}blitz, Susanna and Tronci, Enrico and Mancini, Toni and Salvo, Ivano and Alimguzhin, Vadim and Mari, Federico and Melatti, Igor and Massini, Annalisa and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian and Leeners, Brigitte}, title = {An Integrative Approach for Model Driven Computation of Treatments in Reproductive Medicine}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57103}, abstract = {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.}, language = {en} } @misc{Dierkes, author = {Dierkes, Thomas}, title = {Construction of ODE systems from time series data by a highly flexible modelling approach}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56768}, abstract = {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].}, language = {en} } @article{Dierkes, author = {Dierkes, Thomas}, title = {Construction of ODE systems from time series data by a highly flexible modelling approach}, series = {ArXiv e-prints}, volume = {math.NA 1512.03357}, journal = {ArXiv e-prints}, abstract = {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.}, language = {en} } @inproceedings{EhrigDierkesSchaeferetal., author = {Ehrig, Rainald and Dierkes, Thomas and Sch{\"a}fer, Stefan and R{\"o}blitz, Susanna and Tronci, Enrico and Mancini, Toni and Salvo, Ivano and Alimguzhin, Vadim and Mari, Federico and Melatti, Igor and Massini, Annalisa and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian and Leeners, Brigitte}, title = {An integrative approach for model driven computation of treatments in reproductive medicine}, series = {BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India}, booktitle = {BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India}, language = {en} } @misc{DierkesWadeNowaketal.2011, author = {Dierkes, Thomas and Wade, Moritz and Nowak, Ulrich and R{\"o}blitz, Susanna}, title = {BioPARKIN - Biology-related Parameter Identification in Large Kinetic Networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-12706}, number = {11-15}, year = {2011}, abstract = {Modelling, parameter identification, and simulation play an important r{\^o}le 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.}, language = {en} } @inproceedings{ManciniSalvoMarietal., author = {Mancini, Toni and Salvo, Ivano and Mari, Federico and Melatti, Igor and Massini, Annalisa and Sinisi, Stefano and Tronci, Enrico and Davi, Francesco and Dierkes, Thomas and Ehrig, Rainald and R{\"o}blitz, Susanna and Leeners, Brigitte and Kr{\"u}ger, Tillmann H. C. and Egli, Marcel and Ille, Fabian}, title = {Patient-Specific Models from Inter-Patient Biological Models and Clinical Records}, series = {Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014)}, booktitle = {Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014)}, pages = {207 -- 214}, language = {en} } @article{DierkesRoeblitzWadeetal.2013, author = {Dierkes, Thomas and R{\"o}blitz, Susanna and Wade, Moritz and Deuflhard, Peter}, title = {Parameter identification in large kinetic networks with BioPARKIN}, series = {CoRR - Computing Research Repository - arXiv.org}, volume = {abs/1303.4928}, journal = {CoRR - Computing Research Repository - arXiv.org}, year = {2013}, language = {en} } @article{DierkesOrtmann, author = {Dierkes, Thomas and Ortmann, Karl Michael}, title = {On the efficient utilisation of duration}, series = {Insurance: Mathematics and Economics}, volume = {60}, journal = {Insurance: Mathematics and Economics}, doi = {10.1016/j.insmatheco.2014.11.002}, pages = {29 -- 37}, abstract = {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.}, language = {en} }