{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2801956af6fd7868040c13581eeb42f3b/hermann", "tags" : [ "diss","forschungsdaten","interessant","reusability","software" ], "intraHash" : "801956af6fd7868040c13581eeb42f3b", "interHash" : "530f5354962af5abc72f65745e0f6f62", "label" : "Constructing and analysing dynamic models with modelbase v1.2.3: a\r\n software update", "user" : "hermann", "description" : "", "date" : "2021-05-27 10:24:42", "changeDate" : "2021-05-27 08:24:42", "count" : 1, "pub-type": "article", "journal": "BMC BIOINFORMATICS","publisher":"BMC","address":"CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND", "year": "2021", "url": "", "author": [ "Marvin van Aalst","Oliver Ebenhoeh","Anna Matuszynska" ], "authors": [ {"first" : "Marvin", "last" : "van Aalst"}, {"first" : "Oliver", "last" : "Ebenhoeh"}, {"first" : "Anna", "last" : "Matuszynska"} ], "volume": "22","number": "1","abstract": "BackgroundComputational mathematical models of biological and biomedical\r\n systems have been successfully applied to advance our understanding of\r\n various regulatory processes, metabolic fluxes, effects of drug\r\n therapies, and disease evolution and transmission. Unfortunately,\r\n despite community efforts leading to the development of SBML and the\r\n BioModels database, many published models have not been fully exploited,\r\n largely due to a lack of proper documentation or the dependence on\r\n proprietary software. To facilitate the reuse and further development of\r\n systems biology and systems medicine models, an open-source toolbox that\r\n makes the overall process of model construction more consistent,\r\n understandable, transparent, and reproducible is desired.Results and\r\n discussionWe provide an update on the development of modelbase, a free,\r\n expandable Python package for constructing and analysing ordinary\r\n differential equation-based mathematical models of dynamic systems. It\r\n provides intuitive and unified methods to construct and solve these\r\n systems. Significantly expanded visualisation methods allow for\r\n convenient analysis of the structural and dynamic properties of models.\r\n After specifying reaction stoichiometries and rate equations modelbase\r\n can automatically assemble the associated system of differential\r\n equations. A newly provided library of common kinetic rate laws reduces\r\n the repetitiveness of the computer programming code. modelbase is also\r\n fully compatible with SBML. Previous versions provided functions for the\r\n automatic construction of networks for isotope labelling studies. Now,\r\n using user-provided label maps, modelbase v1.2.3 streamlines the\r\n expansion of classic models to their isotope-specific versions. Finally,\r\n the library of previously published models implemented in modelbase is\r\n growing continuously. Ranging from photosynthesis to tumour cell growth\r\n to viral infection evolution, all these models are now available in a\r\n transparent, reusable and unified format through\r\n modelbase.ConclusionWith this new Python software package, which is\r\n written in currently one of the most popular programming languages, the\r\n user can develop new models and actively profit from the work of others.\r\n modelbase enables reproducing and replicating models in a consistent,\r\n tractable and expandable manner. Moreover, the expansion of models to\r\n their isotopic label-specific versions enables simulating label\r\n propagation, thus providing quantitative information regarding network\r\n topology and metabolic fluxes.", "author-email" : "anna.matuszynska@hhu.de", "language" : "English", "oa" : "DOAJ Gold, Green Published", "affiliation" : "Matuszynska, A (Corresponding Author), CEPLAS Cluster Excellence Plant Sci, Univ Str 1, D-40225 Dusseldorf, Germany.\r\n van Aalst, Marvin; Ebenhoeh, Oliver; Matuszynska, Anna, Heinrich Heine Univ, Inst Quantitat & Theoret Biol, Univ Str 1, D-40225 Dusseldorf, Germany.\r\n Ebenhoeh, Oliver; Matuszynska, Anna, CEPLAS Cluster Excellence Plant Sci, Univ Str 1, D-40225 Dusseldorf, Germany.", "usage-count-last-180-days" : "0", "web-of-science-categories" : "Biochemical Research Methods; Biotechnology & Applied Microbiology;\r\n Mathematical & Computational Biology", "article-number" : "203", "number-of-cited-references" : "45", "research-areas" : "Biochemistry & Molecular Biology; Biotechnology & Applied\r\n Microbiology; Mathematical & Computational Biology", "funding-text" : "Open Access funding enabled and organized by Projekt DEAL. This work was\r\n funded by the Deutsche Forschungsgemeinschaft (DFG, German Research\r\n Foundation) under Germanys Excellence Strategy-EXC-2048/1-project ID\r\n 390686111 (OE, AM), EU's Horizon 2020 research and innovation programme\r\n under the Grant Agreement 862087 (MvA), and Deutsche\r\n Forschungsgemeinschaft Research Grant-project ID 420069095 (AM). The\r\n funding bodies did not play any role in the design of the study nor\r\n collection, analysis, and interpretation of data nor in writing the\r\n manuscript.", "funding-acknowledgement" : "Projekt DEAL; Deutsche Forschungsgemeinschaft (DFG, German Research\r\n Foundation)German Research Foundation (DFG) [390686111]; EU's Horizon\r\n 2020 research and innovation programme [862087]; Deutsche\r\n ForschungsgemeinschaftGerman Research Foundation (DFG) [420069095]", "times-cited" : "0", "issn" : "1471-2105", "orcid-numbers" : "Matuszynska, Anna/0000-0003-0882-6088", "usage-count-since-2013" : "0", "doc-delivery-number" : "RQ6QX", "da" : "2021-05-27", "journal-iso" : "BMC Bioinformatics", "keywords-plus" : "SYSTEMS", "unique-id" : "ISI:000642542300003", "doi" : "10.1186/s12859-021-04122-7", "bibtexKey": "vanaalst2021constructing" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f6dbb3004ea1bb6414aadcce70225900/hermann", "tags" : [ "diss","documentation","forschungsdaten","reusability","software" ], "intraHash" : "f6dbb3004ea1bb6414aadcce70225900", "interHash" : "3dace87e232cc43887d37e9e3814f0a7", "label" : "Open science in practice: Learning integrated modeling of coupled\r\n surface-subsurface flow processes from scratch", "user" : "hermann", "description" : "", "date" : "2021-03-01 06:50:48", "changeDate" : "2021-03-01 05:50:48", "count" : 1, "pub-type": "article", "journal": "EARTH AND SPACE SCIENCE","publisher":"AMER GEOPHYSICAL UNION","address":"2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA", "year": "2016", "url": "", "author": [ "Xuan Yu","Christopher J. Duffy","Alain N. Rousseau","Gopal Bhatt","Alvaro Pardo Alvarez","Dominique Charron" ], "authors": [ {"first" : "Xuan", "last" : "Yu"}, {"first" : "Christopher J.", "last" : "Duffy"}, {"first" : "Alain N.", "last" : "Rousseau"}, {"first" : "Gopal", "last" : "Bhatt"}, {"first" : "Alvaro Pardo", "last" : "Alvarez"}, {"first" : "Dominique", "last" : "Charron"} ], "volume": "3","number": "5","pages": "190-206","abstract": "Integrated modeling of coupled surface-subsurface flow and ensuing role\r\n in diverse Earth system processes is of current research interest to\r\n characterize nonlinear rainfall-runoff response and also to understand\r\n land surface energy balances, biogeochemical processes, geomorphological\r\n dynamics, etc. A growing number of complex models have been developed\r\n for water-related research, and many of these are made available to the\r\n Earth science community. However, relatively few resources have been\r\n made accessible to the potentially large group of Earth science and\r\n engineering users. New users have to invest an extraordinary effort to\r\n study the models. To provide a stimulating experience focusing on the\r\n learning curve of integrated modeling of coupled surface-subsurface\r\n flow, we describe use cases of an open source model, the Penn State\r\n Integrated Hydrologic Model, PIHM. New users were guided through data\r\n processing and model application by reproducing a numerical benchmark\r\n problem and a real-world watershed simulation. Specifically, we document\r\n the PIHM application and its computational workflow to enable intuitive\r\n understanding of coupled surface-subsurface flow processes. In addition,\r\n we describe the user experience as important evidence of the\r\n significance of reusability. The interaction shows that documentation of\r\n data, software, and computational workflow in research papers is a\r\n promising method to foster open scientific collaboration and reuse. This\r\n study demonstrates how open science practice in research papers would\r\n promote the utility of open source software. Addressing such open\r\n science practice in publications would promote the utility of journal\r\n papers. Further, popularization of such practice will require\r\n coordination among research communities, funding agencies, and journals.", "author-email" : "xuan@udel.edu", "language" : "English", "researcherid-numbers" : "Yu, Xuan/O-3449-2014", "oa" : "DOAJ Gold, Green Accepted", "affiliation" : "Yu, X (Corresponding Author), Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n Yu, Xuan, Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n Duffy, Christopher J.; Bhatt, Gopal, Penn State Univ, Dept Civil & Environm Engn, University Pk, PA 16802 USA.\r\n Rousseau, Alain N.; Alvarez, Alvaro Pardo; Charron, Dominique, Univ Quebec, Inst Natl Rech Sci, Ctr Eau Terre Environm, INRS ETE, Quebec City, PQ, Canada.", "usage-count-last-180-days" : "0", "web-of-science-categories" : "Astronomy & Astrophysics; Geosciences, Multidisciplinary", "number-of-cited-references" : "92", "research-areas" : "Astronomy & Astrophysics; Geology", "funding-text" : "All data for this paper are properly cited and referred to in the\r\n reference list. More details of the data are available upon request from\r\n the corresponding author (xuan@udel.edu). This work was supported by NSF\r\n grants IIA-1301765, IIS-1344272, ICER-1343800, and ICER-1440323 and\r\n Shale Hills-Susquehanna Critical Zone Observatory (EAR-0725019,\r\n EAR-1239285, and EAR-1331726). The authors thank the EarthCube OntoSoft\r\n leadership for initiating the Geoscience Papers of the Future program\r\n and the early career advisory committee members. The manuscript\r\n benefited from conversations facilitated by the EarthCube Distinguished\r\n Lecturer Program. The authors also thank Yolanda Gil of University of\r\n Southern California for the insightful discussions and comments on the\r\n manuscript. We also want to thank Ibrahim Demir from University of Iowa\r\n and Runjian Wu from University of Arizona for their help with\r\n proofreading. We are very grateful for the constructive comments from\r\n reviewer Christopher Hutton and an anonymous reviewer on the earlier\r\n versions of the manuscript.", "funding-acknowledgement" : "NSFNational Science Foundation (NSF) [IIA-1301765, IIS-1344272,\r\n ICER-1343800, ICER-1440323]; Shale Hills-Susquehanna Critical Zone\r\n Observatory [EAR-0725019, EAR-1239285, EAR-1331726]; Directorate For\r\n GeosciencesNational Science Foundation (NSF)NSF - Directorate for\r\n Geosciences (GEO) [1331726] Funding Source: National Science\r\n Foundation; Division Of Earth SciencesNational Science Foundation\r\n (NSF)NSF - Directorate for Geosciences (GEO) [1331726] Funding Source:\r\n National Science Foundation; Office of Integrative ActivitiesNational\r\n Science Foundation (NSF)NSF - Office of the Director (OD) [1301765]\r\n Funding Source: National Science Foundation; Office Of The\r\n DirectorNational Science Foundation (NSF)NSF - Office of the Director\r\n (OD) [1301765] Funding Source: National Science Foundation", "times-cited" : "11", "issn" : "2333-5084", "orcid-numbers" : "Yu, Xuan/0000-0002-9055-7923\r\n Duffy, Christopher/0000-0003-0080-6445\r\n Pardo Alvarez, Alvaro/0000-0003-0302-9856\r\n Rousseau, Alain N./0000-0002-3439-2124\r\n Charron, Dominique/0000-0002-8494-1152", "usage-count-since-2013" : "11", "doc-delivery-number" : "DU9XO", "da" : "2021-03-01", "journal-iso" : "Earth Space Sci.", "keywords-plus" : "DISTRIBUTED COMPUTING ENVIRONMENT; HYDROLOGIC MODEL; CLIMATE-CHANGE;\r\n OPPORTUNITIES; SYSTEM; WORKFLOWS; GEOMORPHOLOGY; RESEARCHERS;\r\n CHALLENGES; FEEDBACKS", "unique-id" : "ISI:000382571700001", "doi" : "10.1002/2015EA000155", "bibtexKey": "yu2016science" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24ca27c08adf7ea5e041ecda8b6be91ad/hermann", "tags" : [ "diss","documentation","reusability","software" ], "intraHash" : "4ca27c08adf7ea5e041ecda8b6be91ad", "interHash" : "3bdee2fd90af2b0755b4c42829a6d1b6", "label" : "Measuring the reusability of software components using static analysis metrics and reuse rate information", "user" : "hermann", "description" : "", "date" : "2021-02-26 07:33:26", "changeDate" : "2021-02-26 06:33:26", "count" : 2, "pub-type": "article", "journal": "Journal of Systems and Software","publisher":"Elsevier BV", "year": "2019", "url": "https://doi.org/10.1016%2Fj.jss.2019.110423", "author": [ "Michail D. Papamichail","Themistoklis Diamantopoulos","Andreas L. Symeonidis" ], "authors": [ {"first" : "Michail D.", "last" : "Papamichail"}, {"first" : "Themistoklis", "last" : "Diamantopoulos"}, {"first" : "Andreas L.", "last" : "Symeonidis"} ], "volume": "158","pages": "110423", "doi" : "10.1016/j.jss.2019.110423", "bibtexKey": "papamichail2019measuring" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2bf994cc36055fa648b6d2f9bf35cf214/hermann", "tags" : [ "Deployment","Reproducibility","Research","Reusability","TOSCA","lebenslauf","myown","projekt","publist","roar" ], "intraHash" : "bf994cc36055fa648b6d2f9bf35cf214", "interHash" : "40fe10413905f7ec7836126a296d8120", "label" : "Towards Deployable Research Object Archives Based on TOSCA", "user" : "hermann", "description" : "", "date" : "2019-04-10 16:09:18", "changeDate" : "2022-05-13 14:41:26", "count" : 2, "pub-type": "inproceedings", "booktitle": "Papers From the 12th Advanced Summer School of Service-Oriented Computing (SummerSoC 2018)","publisher":"IBM Research Division", "year": "2018", "url": "https://www.iaas.uni-stuttgart.de/publications/INPROC-2018-44-Towards-Deployable-Research-Object-Archives-Based-on-TOSCA.pdf", "author": [ "Michael Zimmermann","Uwe Breitenbücher","Jasmin Guth","Sibylle Hermann","Frank Leymann","Karoline Saatkamp" ], "authors": [ {"first" : "Michael", "last" : "Zimmermann"}, {"first" : "Uwe", "last" : "Breitenbücher"}, {"first" : "Jasmin", "last" : "Guth"}, {"first" : "Sibylle", "last" : "Hermann"}, {"first" : "Frank", "last" : "Leymann"}, {"first" : "Karoline", "last" : "Saatkamp"} ], "pages": "31--42","abstract": "In science, reproducibility means that a scientific experiment can be repeated\r\n by another scientist with the same result. This is of particular importance to\r\n verify the results as well as to show the usefulness and reusability for\r\n further research. However, the exclusive publication of the research results in\r\n a scientific journal is usually not sufficient. In addition to research\r\n results, also research data as well as research software need to be published\r\n and made public available in order to enable researcher to gain new insights\r\n and thus advance research. However, the reproducibility and reusability of\r\n research data and research software typically is hindered by several barriers.\r\n Therefore, this work intends to first provide an overview of the current\r\n situation and issues in this particular topic and furthermore sketch our vision\r\n of standards-based Research Object Archives containing scientific publications,\r\n software, data, metadata and licenses in order to tackle the existing problems.", "ee" : "https://www.2018.summersoc.eu/", "language" : "Englisch", "cr-category" : "C.2.4 Distributed Systems,\r\n D.2.7 Software Engineering Distribution, Maintenance, and Enhancement,\r\n H.3.7 Digital Libraries", "department" : "Universität Stuttgart, Institut für Architektur von Anwendungssystemen", "bibtexKey": "zimmermann2018towards" } ] }