{ "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" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/4828046de63245ddce111201198e6c41/diglezakis", "tags" : [ "forschungsdaten","provenance","metadata","workflow","scientific" ], "intraHash" : "4828046de63245ddce111201198e6c41", "label" : "The ProvONE Data Model for Scientific Workflow Provenance", "user" : "diglezakis", "description" : "ProvONE aims to provide the fundamental information required to understand and analyze scientific workflow-based computational experiments.", "date" : "2018-05-11 10:33:23", "changeDate" : "2018-05-11 08:33:23", "count" : 1, "url" : "http://jenkins-1.dataone.org/jenkins/view/Documentation%20Projects/job/ProvONE-Documentation-trunk/ws/provenance/ProvONE/v1/provone.html" } , { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/1d54ac25d221a923bbe35b5320793b6b/diglezakis", "tags" : [ "software","scientific","learning","lessons" ], "intraHash" : "1d54ac25d221a923bbe35b5320793b6b", "label" : "Our Lessons", "user" : "diglezakis", "description" : "Videos von Sofware Carpentry-Veranstaltungen", "date" : "2018-03-20 11:41:33", "changeDate" : "2018-03-20 10:41:33", "count" : 1, "url" : "https://software-carpentry.org/lessons/" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/287e551163b741a273e80630495b658d1/diglezakis", "tags" : [ "provenance","metadata","scientific","workflows" ], "intraHash" : "87e551163b741a273e80630495b658d1", "interHash" : "dbc657711d758134c92c99bc29883385", "label" : "Provenance and Scientific Workflows: Challenges and Opportunities", "user" : "diglezakis", "description" : "", "date" : "2018-11-27 11:47:45", "changeDate" : "2018-11-27 10:47:45", "count" : 2, "pub-type": "inproceedings", "booktitle": "Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data","series": "SIGMOD '08","publisher":"ACM","address":"New York, NY, USA", "year": "2008", "url": "http://doi.acm.org/10.1145/1376616.1376772", "author": [ "Susan B. Davidson","Juliana Freire" ], "authors": [ {"first" : "Susan B.", "last" : "Davidson"}, {"first" : "Juliana", "last" : "Freire"} ], "pages": "1345--1350", "acmid" : "1376772", "isbn" : "978-1-60558-102-6", "numpages" : "6", "location" : "Vancouver, Canada", "doi" : "10.1145/1376616.1376772", "bibtexKey": "Davidson:2008:PSW:1376616.1376772" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22c57d9969ea298d801eac61b26dd6e02/diglezakis", "tags" : [ "software","scientific" ], "intraHash" : "2c57d9969ea298d801eac61b26dd6e02", "interHash" : "6ea6b25d260ec9a110aefe07b50b3db1", "label" : "Software Design for Empowering Scientists", "user" : "diglezakis", "description" : "", "date" : "2017-09-12 16:27:51", "changeDate" : "2017-09-12 14:27:51", "count" : 2, "pub-type": "article", "journal": "IEEE Software", "year": "2009", "url": "", "author": [ "D. De Roure","C. Goble" ], "authors": [ {"first" : "D. De", "last" : "Roure"}, {"first" : "C.", "last" : "Goble"} ], "volume": "26","number": "1","pages": "88-95","abstract": "Scientific research is increasingly digital. Some activities, such as data analysis, search, and simulation, can be accelerated by letting scientists write workflows and scripts that automate routine activities. These capture pieces of the scientific method that scientists can share. The Taverna Workbench, a widely deployed scientific-workflow-management system, together with the myExperiment social Web site for sharing scientific experiments, follow six principles of designing software for adoption by scientists and six principles of user engagement.", "issn" : "0740-7459", "doi" : "10.1109/MS.2009.22", "bibtexKey": "4721191" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2998132ad5963499288571f56f9cdfa20/diglezakis", "tags" : [ "softwareEngineering","literatureReview","software","scientific","research" ], "intraHash" : "998132ad5963499288571f56f9cdfa20", "interHash" : "e7a1ce46d5814640dcacf5cfdcc81a50", "label" : "DEVELOPMENT OF SCIENTIFIC SOFTWARE: A SYSTEMATIC MAPPING, A BIBLIOMETRICS STUDY, AND A PAPER REPOSITORY", "user" : "diglezakis", "description" : "DEVELOPMENT OF SCIENTIFIC SOFTWARE: A SYSTEMATIC MAPPING, A BIBLIOMETRICS STUDY, AND A PAPER REPOSITORY | International Journal of Software Engineering and Knowledge Engineering , Vol 23, No 04 | World Scientific", "date" : "2017-09-12 16:10:46", "changeDate" : "2017-09-12 14:10:46", "count" : 2, "pub-type": "article", "journal": "International Journal of Software Engineering and Knowledge Engineering", "year": "2013", "url": "http://www.worldscientific.com/doi/abs/10.1142/S0218194013500137", "author": [ "ROSHANAK FARHOODI","VAHID GAROUSI","DIETMAR PFAHL","JONATHAN SILLITO" ], "authors": [ {"first" : "ROSHANAK", "last" : "FARHOODI"}, {"first" : "VAHID", "last" : "GAROUSI"}, {"first" : "DIETMAR", "last" : "PFAHL"}, {"first" : "JONATHAN", "last" : "SILLITO"} ], "volume": "23","number": "04","pages": "463-506","abstract": "

Scientific and engineering research is heavily dependent on effective development and use of software artifacts. Many of these artifacts are produced by the scientists themselves, rather than by trained software engineers. To address the challenges in this area, a research community often referred to as \"Development of Scientific Software\" has emerged in the last few decades. As this research area has matured, there has been a sharp increase in the number of papers and results made available, and it has thus become important to summarize and provide an overview about those studies. Through a systematic mapping and bibliometrics study, we have reviewed 130 papers in this area. We present the results of our study in this paper. Also we have made the mapping data available on an online repository which is planned to be updated on a regular basis. The results of our study seem to suggest that many software engineering techniques and activities are being used in the development of scientific software. However, there is still a need for further exploration of the usefulness of specific software engineering techniques (e.g., regarding software maintenance, evolution, refactoring, re(v)-engineering, process and project management) in the scientific context. It is hoped that this article will help (new) researchers get an overview of the research space and help them to understand the trends in the area.

", "doi" : "10.1142/S0218194013500137", "eprint" : "http://www.worldscientific.com/doi/pdf/10.1142/S0218194013500137", "bibtexKey": "doi:10.1142/S0218194013500137" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/20e982958effa54da3d9e5395fff968dc/diglezakis", "tags" : [ "software","scientific","research" ], "intraHash" : "0e982958effa54da3d9e5395fff968dc", "interHash" : "cfcf0b9fbcfb3923b5f9e675bb9d6761", "label" : "How do scientists develop and use scientific software?", "user" : "diglezakis", "description" : "", "date" : "2017-09-12 16:04:41", "changeDate" : "2017-09-12 14:04:41", "count" : 3, "pub-type": "article", "year": "2009", "url": "http://dx.doi.org/10.1109/SECSE.2009.5069155", "author": [ "Jo Erskine Hannay","Hans Petter Langtangen","Carolyn MacLeod","Dietmar Pfahl","Janice Singer","Greg Wilson" ], "authors": [ {"first" : "Jo Erskine", "last" : "Hannay"}, {"first" : "Hans Petter", "last" : "Langtangen"}, {"first" : "Carolyn", "last" : "MacLeod"}, {"first" : "Dietmar", "last" : "Pfahl"}, {"first" : "Janice", "last" : "Singer"}, {"first" : "Greg", "last" : "Wilson"} ], "pages": "1-8","abstract": "New knowledge in science and engineering relies increasingly on results produced by scientific software. Therefore, knowing how scientists develop and use software in their research is critical to assessing the necessity for improving current development practices and to making decisions about the future allocation of resources. To that end, this paper presents the results of a survey conducted online in October-December 2008 which received almost 2000 responses. Our main conclusions are that (1) the knowledge required to develop and use scientific software is primarily acquired from peers and through self-study, rather than from formal education and training; (2) the number of scientists using supercomputers is small compared to the number using desktop or intermediate computers; (3) most scientists rely primarily on software with a large user base; (4) while many scientists believe that software testing is important, a smaller number believe they have sufficient understanding about testing concepts; and (5) that there is a tendency for scientists to rank standard software engineering concepts higher if they work in large software development projects and teams, but that there is no uniform trend of association between rank of importance of software engineering concepts and project/team size. \r\n\r\n(1) How Do Scientists Develop and Use Scientific Software?. Available from: https://www.researchgate.net/publication/232632350_How_Do_Scientists_Develop_and_Use_Scientific_Software [accessed Sep 12, 2017].", "doi" : "10.1109/SECSE.2009.5069155", "bibtexKey": "hannay2009scientists" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f9638bd803ce59c54e6a0bd41a9bf515/diglezakis", "tags" : [ "software","workflow","scientific","softwareLizenzMotivation","repository" ], "intraHash" : "f9638bd803ce59c54e6a0bd41a9bf515", "interHash" : "2b31e514b2bc2caf54d7849e7c3c882e", "label" : "The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences", "user" : "diglezakis", "description" : "The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences | SpringerLink", "date" : "2017-09-12 14:04:34", "changeDate" : "2017-09-12 12:04:34", "count" : 1, "pub-type": "article", "journal": "Behavior Research Methods", "year": "2016", "url": "https://doi.org/10.3758/s13428-015-0616-x", "author": [ "Pär Nyström","Terje Falck-Ytter","Gustaf Gredebäck" ], "authors": [ {"first" : "Pär", "last" : "Nyström"}, {"first" : "Terje", "last" : "Falck-Ytter"}, {"first" : "Gustaf", "last" : "Gredebäck"} ], "volume": "48","number": "2","pages": "542--552","abstract": "This article describes a new open source scientific workflow system, the TimeStudio Project, dedicated to the behavioral and brain sciences. The program is written in MATLAB and features a graphical user interface for the dynamic pipelining of computer algorithms developed as TimeStudio plugins. TimeStudio includes both a set of general plugins (for reading data files, modifying data structures, visualizing data structures, etc.) and a set of plugins specifically developed for the analysis of event-related eyetracking data as a proof of concept. It is possible to create custom plugins to integrate new or existing MATLAB code anywhere in a workflow, making TimeStudio a flexible workbench for organizing and performing a wide range of analyses. The system also features an integrated sharing and archiving tool for TimeStudio workflows, which can be used to share workflows both during the data analysis phase and after scientific publication. TimeStudio thus facilitates the reproduction and replication of scientific studies, increases the transparency of analyses, and reduces individual researchers' analysis workload. The project website ( http://timestudioproject.com ) contains the latest releases of TimeStudio, together with documentation and user forums.", "issn" : "1554-3528", "doi" : "10.3758/s13428-015-0616-x", "bibtexKey": "Nyström2016" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/252258c43ea1cd7975786fbbc2a61182e/diglezakis", "tags" : [ "software","scientific","goodPractice" ], "intraHash" : "52258c43ea1cd7975786fbbc2a61182e", "interHash" : "89d06301d19fe097e96f032d7499f4e1", "label" : "Good enough practices in scientific computing", "user" : "diglezakis", "description" : "", "date" : "2017-09-12 12:57:03", "changeDate" : "2017-09-12 10:57:03", "count" : 3, "pub-type": "article", "journal": "PLOS Computational Biology","publisher":"Public Library of Science", "year": "2017", "url": "https://doi.org/10.1371/journal.pcbi.1005510", "author": [ "Greg Wilson","Jennifer Bryan","Karen Cranston","Justin Kitzes","Lex Nederbragt","Tracy K. Teal" ], "authors": [ {"first" : "Greg", "last" : "Wilson"}, {"first" : "Jennifer", "last" : "Bryan"}, {"first" : "Karen", "last" : "Cranston"}, {"first" : "Justin", "last" : "Kitzes"}, {"first" : "Lex", "last" : "Nederbragt"}, {"first" : "Tracy K.", "last" : "Teal"} ], "volume": "13","number": "6","pages": "1-20","abstract": "Author summary Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.", "doi" : "10.1371/journal.pcbi.1005510", "bibtexKey": "10.1371/journal.pcbi.1005510" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/291d0c94e83943bb87f0f3fb8c41aeb83/diglezakis", "tags" : [ "development","software","scientific" ], "intraHash" : "91d0c94e83943bb87f0f3fb8c41aeb83", "interHash" : "e31037c468a128e1e245be8eafb0d34f", "label" : "Channeling Community Contributions to Scientific Software: A Sprint Experience", "user" : "diglezakis", "description" : "Channeling Community Contributions to Scientific Software: A Sprint Experience", "date" : "2017-09-12 08:54:17", "changeDate" : "2017-09-12 06:54:17", "count" : 1, "pub-type": "article", "journal": "J Open Res Softw", "year": "2016", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5104275/", "author": [ "M R Crusoe","C T Brown" ], "authors": [ {"first" : "M R", "last" : "Crusoe"}, {"first" : "C T", "last" : "Brown"} ], "volume": "4","number": "1","abstract": "In 2014, the khmer software project participated in a two-day global sprint coordinated by the Mozilla Science Lab. We offered a mentored experience in contributing to a scientific software project for anyone who was interested. We provided entry-level tasks and worked with contributors as they worked through our development process. The experience was successful on both a social and a technical level, bringing in 13 contributions from 9 new contributors and validating our development process. In this experience paper we describe the sprint preparation and process, relate anecdotal experiences, and draw conclusions about what other projects could do to enable a similar outcome. The khmer software is developed openly at http://github.com/dib-lab/khmer/.", "pmid" : "27840675", "doi" : "10.5334/jors.96", "bibtexKey": "Crusoe:2016:J-Open-Res-Softw:27840675" } ] }