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Possible Titles

Open Science in Practice: A Classification of Tools and Workflows in a Process-based Model

Applications in and for Open Science

Transforming the Scientific Method: Open Science Tools in Practice


  • Bestandsaufnahme Open Science Tools
  • General Research Workflow: welche Tools sind nötig um eine offene Wissenschaft zu betreiben?
  • Welche Tools gibt es für die versch. WF Steps?
  • Wie ist ihre Anwendbarkeit; wie sind sie für best. Steps/versch. Forschungsrichtungen adaptiert?
  • Interoperabilität?


For Open Science to become a sustainable and widely adopted reality, there is the need to develop adequate virtual research environments and tools, which enable the transfer of entire workflows to the Web. In this paper we take a closer look at currently available Open Science applications and services, which can be used for supporting researchers in specific workflow steps. We have reviewed selected tools in terms of their applicability to the steps of a generic research workflow and their interoperability. Our focus lies on the core workflow steps of many empirical disciplines, namely Discovery, Data Analysis, and Writing & Publishing, but also Preparation/Management, Outreach and Assessment will be touched. The main goal of this paper is to identify current gaps and make some indications for future development of Open Science tools and services/research environments.


Open Science is a recent approach in research which is increasingly being supported, e.g. by the European Commission. Open Science can be defined as "opening up the research process by making all of its outcomes, and the way in which these outcomes were achieved, publicly available on the World Wide Web." Kraker et al. 2011

Not only it leads to a more open communication of research processes and results via the Web. It also offers the possibility to create new virtual research environments where researchers can collaborate and communicate by means of Web 2.0 applications and services. For Open Science to become a sustainable and widely adopted reality, however, there is the need to develop adequate virtual research environments and tools, which enable the transfer of entire research workflows to the Web. The goal of such infrastructure should be to increase and make online collaboration more practicable for researchers of any discipline. The tools should respond to the researchers’ specific needs and preferences in terms of functionality and usability, as well as of functionalities required for their specific research area.

Due to their heterogeneity and complexity, considering various research area specific workflows lays outside the scope of this paper.

Process-based model of the scientific workflow

Our paper is based on a process-based model of scientific work which we have adapted from Kraker and Lindstaedt 2011. In this model, the main process chain consists of 5 core processes: research design, study development, implementation/data collection, evaluation/data analysis, and publication. Research design denotes the initial phase of the research process where the concept is generated, research questions are formulated, and research methods are established. Study development describes the stage where - depending on the discipline - instruments, analytical frameworks, and/or software is developed. Implementation encompasses the data collection phase, where  fieldwork is conducted, such as observations, case studies, experiments, and surveys, as well as the implementation of software in a certain environment. Evaluation denotes data analysis and interpretation of the data gathered during the implementation process. Finally, publication stands for the production of written outcomes of the aforementioned processes (e.g. conference and journal papers, books and book chapters).

In addition to the five core processes, the model sports 15 support processes. Support processes signify processes that are not part of the main value chain but that are important, and sometimes even necessary for core processes to work. Some of the more general support processes, such as communication, collaboration, and networking are important for all core processes, whilst more specific support processes such as editing are only important to a single core process (publication in that case).

Next to core and support processes, the model contains five management processes. Management processes are processes which create the necessary environment for core and support processes to run. These are: research strategy, including project and publication planning, human resource management, knowledge management, financial management (which involves funding and project acquisition), and resources management, including all other resources such as IT infrastructure and lab equipment.

List of tool- and service-links used for the paper

Preparation, Management

Open Science Framework:

Research Design and Discovery


Study Development, Analysis and Evaluation

Genome Compiler:
Curate Science:
Laboratory Logbook:
Resource Identification Portal:
Sample of Science:
Open Science Grid:
IPython Notebook:
Open Notebook Science Network:


Google Drive:
Collage Authoring Environment:
DOI Citation Formatter:
Open Science Repository:
PeerJ preprints:
Edanz Journal Selector:[underscore]selector
Journal Guide:
Quality Open Access Markets:
BMJ Open:
F1000 Research:
Gene Expression Omnibus (GEO):
Global Biodiversity Information Facility:

Outreach and Assessment

Linked Research:

Open Science: Main Processes/Workflow Steps & associated tools/services

note: all the information about tools are taken from

Overview of main workflow steps and mapping to the process model
  • Preparation
  • Discovery/Design -> Research Design
  • Analysis - > Study Development, Implementation/Data Collection & Evaluation/Data Analysis
  • Publication & Writing -> Publication
  • Outreach
  • Assessment

bold: core workflow steps

Research Design (prev: Discovery/Design)

Literature search, Reference management, Quality assurance, Awareness/Discovery

search literature, data, patents, code via the Web
Examples for field-specific search engines

PubMed: (discovery tool for biomedical sciences)

GenBank: (annotated collection of all publicly available DNA sequences, provided by NCBI)

OpenPHACTS: (open access innovation platform for drug discovery via a semantic web approach)

Examples for multidisciplinary Open Access full text aggregations

Libraccess: (Not-for-profit platform, international and interdisciplinary, full text aggregating open access resources across repositories, to make them widely available.)

Paperity: (multidisciplinary OA aggragation)

OALib (search): (aggregate and index scholarly OA publications)

ResearchPad: (OA search engine/ePub reader )

get access to literature, data, etc. via the Web

HowOpenIsIt? (determine license for journal articles)

Open Access Button: (raises awareness about (lack of) Open Access; offers alternative ways to get paywalled paper (repositories, contact author))

reference management

Mendeley: (reference management, with citing/bibliography options)

Zotero: (reference management, with citing/bibliography options)

RefWorks: (reference management, with citing/bibliography options)

annotate/tag during/after reading (annotating, commenting and tagging tool) (Annotate and collaborate on documents and images)

PeerLibrary: (collaborative annotating; discovery)

software requirements & design

plan & define a study, an experiment

define research question

collaboration on-line

Open Science Framework: (open network of research documents, version control system, collaboration software, project management and registering)

Study Development, Implementation/Data Collection & Evaluation/Data Analysis (prev: Analysis, Development, Implementation)

Software development, Finding the right method, Survey design

Disseminating questionnaires

Disucssing evaluation approaches, Data sharing, Marketplaces for evaluations

conduct experiment
Lab equipment, inventory

Biocompare: (lab equipment reviews)

Selectscience: (independent, online review resource for lab equipment and techniques)

StrainControl: (lab inventory tool)


Wings: (semantic workflow system that assists scientists with the design of computational experiments)

CurateScience: (online platform to facilitate replication by aggregating data/syntax files and enabling curation)

GenomeCompiler: (Genetic design platform (manipulate and design everything from single genes to entire genomes))

Research resources, samples, field-specific

Resource Identification Portal: (providing, discovering and citing research resources (organisms, antibodies, tools) based on RRIDs)

Sample of Science: (Marketplace for (physical) sample sharing. Samples get published and receive DOI)

Lab notebook, logbook

LabFolder: (electronic lab notebook)

LabGuru: (electronic lab notebook)

Laboratory Logbook: (document and manage lab data and metadata)

collect/mine/extract data (Turning web into data (scraping, parsing etc.); not restricted to scholarly use)

PDF Miner: (Extracting information from PDF documents)

ScraperWiki: (extract/scrape tables from PDFs)

WebPlotDigitizer: (Extract data from plots, graphs, maps etc)

develop & implement software

Appsoma: (developing, running and publishing code for science applications)

DHbox: (cloud-based digital humanities lab, pre-equipped w/ IPython, RStudio, Omeka, and NLTK.)

Open Science Grid: (software to support collaborative computing)

create and conduct a survey

Limeservice: (Online survey creating and running)

SocialSci: (data collection platform: design surveys and recruit from participant pool)

Google Forms: (online surveys)

AllTrials: (campaign for preregistration of clinical trials)

perform analysis

Arvados: (Virtual environment enabling reproducibility of data analysis with versioned scripts and tools)

Galaxy: (online data manipulation and analysis, for biomedical research but in principle field agnostic)

GenePattern: (genomic analysis platform that provides access to hundreds of genomics tools.)

IPython Notebooks: (editing document format that allows combination of executable code, txt, mathematics, plots and media; parallel computing)

ROpenSci: (packages to connect data/literature/metric/visulaization etc. repositories/search engines to R using APIs)

formulate hypotheses -> collaboration on-line, write

share notebooks, protocols, workflows, etc.
Lab notebooks

Open Notebook Science: of 1st: (open (lab)notebook)

OpenWetWare: (lab notebooks and community)

HiveBench: (electronic lab notebook with some Open protocols)

LabArchives: (electronic lab notebook (commercial provider); possibility to publish data publicly)


Benchfly: (video protocols and video platform for scientists)

Benchling: (data management and collaboration platform to create, find, and discuss protocols)

MyExperiment: (sharing workflows, esp. in bioinformatics)

e.g. software evaluation, evaluation of the survey, evaluation of data

share data with trusted peers

Publication (prev: Publication & Writing)

Writing, Publishing

visualise -> this might also fit into the former step of data analysis...
Charts, Maps, Tables

Datawrapper: (creating charts and maps online)

Google Charts: (create live and interactive charts in your browser)

Google Fusion Tables: (data visualization web application to gather, visualize, and share data tables)

Graphs, Images (create graphs (collaboratively))

Raw: (Open web app to create custom vector-based visualizations using D3.js library )

Image-maps: (making clickable image-maps)


World Map: (Build maps and other geospatial visualizations)


Collage Authoring Environment: (authoring environment for executable publications)

Authorea: (online colloborative writing)

Draft: ((collaboratively) writing and versioning drafts)

Google Drive/Docs: (online text/spreadsheet/presentation editing)

Overleaf: (broad platform for (collaborative) writing with easy links for reviewing and publishing [was: WriteLaTeX])

Penflip: (collaborative writing and version control)

Quip: (oline collaborative writing and document sharing / "productivity app"; also spreadsheets)

ShareLaTeX: (LaTex collaborative editor/sharing platform (paid))


Fore-Cite: (aggreates full text OA for suggesting references to cite + citation context)

Crossref DOI Citation Formatter: (Format citation from DOI) (create permanent links; permalinks are 'vested' by journals and archived by libraries)

WebCite: (storing webpages for permalink for referencing)

Scientific Citations: (Post-publication citation)


AJE (American Journal Experts): (proofreading, translation, editing by PhD students)

Publish & present research results

Archive/share data
Examples for field-specific data archives

Databrary: (data and video sharing for human and animal development research)

DataOne (Data Observation Network for Earth): (distributed framework for open, persistent access to Earth observational data)

Gene Expression Omnibus (GEO): (sharing genomics data)

Global biodiversity information facility Data: (archive biodiversity data)

Knowledge network for Biocomplexity: (Data archiving repository for ecology & environmental science)

Patientslikeme: (Share health experiences and data)

World Data System: (Data archive for geoscience and space science data)

Examples for multi-field data archives

Figshare: (data archiving and sharing)

DataHub: (data repository)

Dryad: (cloud storage and sharing of datasets, CC-0 and article-linked)

Zenodo: (OA repository for EU funded data and publications)

Academic Torrents: (distributed system for sharing large datasets)

re3data: (registry of research data repositories)

Archive/share code

BitBucket: (Sharing code)

Guthub: (code sharing and archiving)

RunMyCode: (Sharing code and data)

Research Compendia: (Share software and data associated with a publication)

Archive/share publications
Examples for multi-field repositories

Open Science Repository: (institution independent OA repository)

ArXiV: (preprint server)

PeerJ preprints: (publish preprint articles (to be submitted to PeerJ but also others (CC-BY))

SSRN: (preprint server)

Examples for field-specific repositories

Europe Pubmed Central: (ful text OA archive in life/health)

PMC (PubMed Central): (full text repository of deposited medical literature)

Archive/share posters

F1000 posters: (poster repository)

Science Open posters: (poster archiving/sharing)

Archive/share presentations

SlideShare: (Share presentations)

Speakerdeck: (Share presentations, upload slides as pdf)

Archive/share videos

SciVee: (science video sharing platform (from journals, conferences, education))

select journal to submit to

Edanz journal selector: (journal selecting for submitting)

Journal Guide: (selection of journals to submit paper to)

Jane: (journal selection support with co-word analysis)

Scientific Journal Finder: (journal recommender based on title and abstract of scientific manuscript in life sciences)

IP Science: (OA journal index with impact factor)

CoFactorScience: (consultancy: workshops, editing, journal selector)

F1000 Research: (immediate and transparent publishing platform, post-publication open-peer-review)

new: Qality Open Access Markets: (scorecards for open access journals)

new: Sherpa/Romeo (service for checking archiving policies & permissions)

pre-publication peer-review & commenting/recommending

BMH Open: (open peer review)

Peerageofscience: (journal independent peer review)

PeerReviewers: (journal independent peer review)

BMJ (British Medical Journal): (Journal with non-anonymous peer review)

Scirate: (rate and comment on ArXiV papers)

Libre Liberating Research: (open peer review)

Other phases (not considered here)

Preparation (e.g. management, project and resources planning & monitoring, funding, reporting)

Outreach (e.g. dissemination, valorise, researcher profile and network)

Assessment (e.g. peer-review (post-publication), impact measure, researcher assessment).

Literature, Sources

Bartling, S., Friesike, S. (2014). Towards Another Scientific Revolution. Opening Science: The Evolving Guide on How the Web is Changing Research, Collaboration and Scholarly Publishing. Retrieved November 13, 2014 from

Bishop, D. (2014). Data sharing: Exciting but scary. :

Burgelman, J.-C. et al. (2010). Science 2.0 (change will happen ...). First Monday 15(7). Retrieved November 27, 2014 from

European Commission (2013). Options for Strengthening Responsible Research and Innovation. :

European Commission (2014 a). Background document. Public Consultation ‘Science 2.0’: Science in transition. Retrieved November 13, 2014 from consultations/science-2.0/background.pdf

Kraker, P., Lindstaedt, S. (2011). Research Practices on the Web in the Field of Technology Enhanced Learning. Proceedings of the ACM WebSci 2011, Koblenz, Germany, 1-3

Kramer, B.; Bosman, J. (2015): 101 Innovations in Scholarly Communication - the Changing Research Workflow. figshare. Retrieved 10:34, May 27, 2015 (GMT)

Kowalczuk, M. (2015). Open data – more obstacles or opportunities? Retrieved March 3, 2015 from

Kuhn, T. (1962). The Structure of Scientific Revolutions. University of Chicago Press.

McDowell, G. et al. (2014). Shaping the Future of Research: a perspective from junior scientists [v1; ref status: awaiting peer review]. F1000Research 2014, 3:291 Last updated: 28 NOV 2014. DOI: 10.12688/f1000research.5878.1

Sitaraman, V. (2015). Science Communication Is Broken. Let's Fix It. Retrieved March 3, 2015 from:

Udell, J. (2015). When Open Access is the norm, how do scientists work together online? Retrieved April 15, 2015 from: (Open Access Spectrum (OAS) guide) (principles for Open Data in science)


Design > Development > Implementation > Evaluation > Publication (Tools auf Workflow-Steps zuordnen)

Tools & Workflows

Research phases

preparation > discovery > analysis > writing > publication > outreach > assessment

Research lifecycle

planning, execution, reporting, archiving, and discovery

Tools, Platforms

400+ Tools and Innovations in Scholarly Communication

Project management, content sharing (Platform: share content and data, citable) (Platform: project management, share content and data) (Platform: data publishing) (collaboration tool, Open Source software and other content) (Software packages allowing access to data repositories)

Collaborative writing/editing (collaborative editor, LaTeX) (collaborative editor, LaTeX) (collaborative editor)

Licensing (CC licensing tool)

Posting Preprints (service for checking archiving policies & permissions) (preprint server for physics, mathematics, and other fields; but not open to all - you need to be recommended by a member to be able to post papers there) (preprint server for biology, life sciences) (preprint service by Peer J)

Open Web Annotation, Post-Publication Review (Tool for post-publication review of papers on Mendeley) (Tool for commenting scientific articles) (Open Web Annotation Tool)

Open Access or not; How Open Is It? (Tool for marking Open Access an non- accessibility and making it visible) (Service to determine license for journal articles)

Choosing an Open Access journal (OA journal index with impact factor) (journal selection tool) (immediate and transparent publishing platform, post-publication open-peer-review)

Impact tracking & Altmetrics (altmetrics) (altmetrics) (altmetrics)


Other (currently down; collaborative planning? tool for students) (prototype testing phase over; open peer review)


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