@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{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 Many of these codes are based on inefficient and mathematically outdated algorithms.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} } @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} } @misc{BehrensBertelmannBoltzeetal., author = {Behrens, Kathrin and Bertelmann, Roland and Boltze, Julia and Ceynowa, Klaus and Christof, J{\"u}rgen and Dierkes, Thomas and Goltz-Fellgiebel, Julia Alexandra and Groß, Matthias and Hammerl, Michaela and Haoua, Marsa and Heermann, Petra and Hoffmann, Cornelia and H{\"o}hnow, Tobias and Koch, Thorsten and Kuberek, Monika and Pampel, Heinz and Putnings, Markus and Rusch, Beate and Sch{\"a}ffler, Hildegard and Schwidder, Jens and S{\"o}llner, Konstanze and Staub, Hedda and Wannick, Eike}, title = {DeepGreen - Open Access Transformation: Eine Handreichung f{\"u}r institutionelle Repositorien}, issn = {1438-0064}, doi = {10.12752/7443}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74438}, abstract = {Mit dem DFG-gef{\"o}rderten Projekt DeepGreen soll eine automatisierte, rechtssichere L{\"o}sung 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 {\"u}berf{\"u}hren. Dabei liegt der Fokus auf den DFG-gef{\"o}rderten und {\"u}berregional 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 Ver{\"o}ffentlichung, der durch die DeepGreen-Datendrehscheibe zugeordneten Artikel, zu erm{\"o}glichen. Die Handreichung basiert auf den bisherigen Erfahrungen der DeepGreen-Projektbeteiligten.}, language = {de} } @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} }