Several additional Tools and Services exist that assist you in your scientific research. Here you can find a selection of science-apps. A summary of useful Science-tools like Software and Web Resources can be found in Science Tools.
- Specific Science-Apps and Apps for administrative work can be found in Science Apps and will be presented in the newly-offered AppClub (AppClub-Details here) - please share further suggestions with us.
Which volumes of a specific ejournal you can access is shown by signal colour in the EZB. (Please note: Articles of fee-based subscribed eJournals - marked "yellow"- are accessible in full text either on Campus or off-campus via connect (/VPN) - if off-campus-usage is not prohibited by the provider. => When you are off-campus please use connect (/VPN).
How to use subscribed content via connect can be found in the connect-guide in Intranet: Bibliothek > Zeitschriften (Intranet) or Bibliothek > Downloads )
Access eJournals on mobile devices via BrowZine:
With the app BrowZine you can search and use eJournals (working on Smartphone, Tablet, Kindle & Laptop/ PC). Browzine enables a fast access to thousands of our licenced eJournals and shows related eJournals.
How to use Browzine is described at our page eJournals
Academia, Mendeley, Researchgate & Co. (Scientific Social Networks)
Use scientific social networks (Academia, Mendeley, Researchgate etc.) to connect with colleagues, discuss specific topics or publications
and share information and/ or content - in case of articles be aware of the sharing conditions (see graphic "Article sharing" and check the conditions via Sherpa/RoMEO).
You're unsure which scientific social network to use? just find out which scientific social network (SSN) suits your needs best and is used by your colleagues.
More or also interested in managing literature (?) > see Endnote, Mendeley & Co. (Reference Management Software)
CreativeCommons, GNU & Co. (Open licences/ offene Lizenzen für Bilder, Daten etc.)
The version of your article influences the copyright and how you're allowed to share it (see grapic Article sharing). If you are the copyright-owner you can define the conditions of your work's reuse. In order to license a scientific work such as data, image etc. via CreativeCommons (CC), GNU, Open Data Commons (ODC) etc. you check which of the licenses best meet your goals/ needs, and then you mark your work in one of the possible ways so that others know that you have chosen to release the work under the terms of that license (e.g. CreativeCommons's licence-choosing-tool ).
Learn more about Open data licensing in EU, USA etc. and in the specific research fields : Guide to Open Data Licensing.
Docoloc & Co. (Plagiarism finding tool)
To identify and prevent plagiarism the Executive Management HZI has licenced for staff members the plagiarism finding tool Docol©c.
For more details on registration for Docol©c and how to use it please visit the Intranetseite Docoloc.
Digitale Identifier für Wissenschaftler (ORCID, ResearcherID, ScopusID..)
Unique researcher identifiers for persons (similar to the content-related digital object identifier/ DOI) make it possible to link the own research activities and outputs to the own researcher identifier - the following are the most important ones:
- ORCID (http://orcid.org/): a subset of the International Standard Name Identifier (ISNI), in addition to members and sponsors, journals, publishers, and other services (as exporting, importing e.g. Pubmed-PMC ORCID claiming tool, Migration services e.g. Mendeley2ORCID, Scopus2ORCID etc.) have included ORCID in their workflows or databases (e.g.. Github). So, include your ORCID identifier on your webpage, when you submit publications, apply for grants, and in any research workflow, to ensure you get credit for your work - more details in the news announcements Are you as a researcher ready to get a researcher ID? (20. März 2015) and ORCID becomes mandatory for some publishers and funders (21. Januar 2016)
- ResearcherID (http://www.researcherid.com/): another solution to the author ambiguity problem introduced by ThomsonReuters (see linking ORCID and ResearcherID)
- ScopusID (see help on Scopus author ID,ORCID and Scopus: Manage your author profile): part of the author details of each publication that is integrated into the database Scopus can be viewed and the author can link Scopus and ORCID or request a correction.
DFN-Terminplaner für Terminkoordination/ for coordination of possible meeting times (https://terminplaner.dfn.de)
Similar to Doodle you can coordinate appoinments but with data security with the DFN scheduler: The DFN scheduler pays special attention to the protection of data on the one hand, and the data economy on the other not choosing to provide additional features.
The DFN scheduler can be used as such without any registration. Moreover, upon access to the DFN scheduler no IP addresses are stored. All data used in the process of scheduling are exclusively stored in Germany with the DFN association, and are not passed onto a third party for any other purpose than the respective appointment being made. Additionally, for each appointment scheduled a date of expiration is required to indicate when the appointment with all its data entered will be deleted automatically.
The DFN scheduler can be used free of charge: start DFN scheduler
DOIs (Digital Object Identifier) are persistent identifier for scientific content (articles, research data etc.). Type or paste a DOI name into the text box (DOI name) and your browser will take you to a Web page (URL) associated with that DOI name.
Via a DOI it might be possible to find an OpenAccess-version auf http://unpaywall.org/ . The Unpaywall-Plugin can be added permanently to your browser. More details on the advantages and the indexed sources on http://unpaywall.org/ and https://www.nature.com/news/unpaywall-finds-free-versions-of-paywalled-papers-1.21765 and http://blogs.lse.ac.uk/impactofsocialsciences/2017/04/04/announcing-unpaywall-unlocking-openaccess-versions-of-paywalled-research-articles-as-you-browse/
Endnote, Mendeley & Co. (Reference Management Software/ Literaturverwaltungssystem)
Endnote: HZI has licenced Endnote (and HIRI has licenced Citavi) as a campus licence which means you can install Endnote on institutional devices like other important Software via Softwarecenter (Start > Microsoft System Center 2012 > Configuration Manager > Softwarecenter).
Focus Endnote: What does Endnote offer to you?
Mendeley: HZI Library offered “Mendeley premium seats” until 30. March 2017 for HZI members, enabling users of the reference management software Mendeley at HZI and Twincore to benefit from numerous enhancements. Up to 500 institutional members were able to upgrade to “Mendeley premium seats” due to Steffi’s participation in the “Mendeley Certification Program for Librarians”. (Upgrade to Mendeley Premium Seats was possible until 30. March 2017 (after that deadline the upgrade possibility was deactivated but upgraders can still use the enhanced Mendeley-Features)
Focus Mendeley: What does Mendeley offer to you? (free Mendeley Basic)
- more details on the core functions and limits of the main important reference management software see
- Literaturverwaltungsprogramme im Vergleich/Comparison of Reference Management Software[TU München, only in German, last update:3. July 2020]: This document compares features, handling and licence and pricing models of reference management applications (Citavi, EndNote, EndNote Web, Zotero, Mendeley, JabRef, Colwiz, Zoterobib). Please feel free to reuse this document and contact TUM University Library for the original data.
- links to different helpdesks of the main important reference management tools see webpage links, section 3) Literaturverwaltung (literature management) & social bookmarking
Collaborative Writing-Tool SciFlow
SciFlow is a web platform for the joint writing of scientific (and other) texts. The Berlin startup securely hosts its servers in Germany. The GDPR conformity distinguishes SciFlow from international competitors such as Authorea or GoogleDocs (those both are not compliant to DSGVO).
The HZI is a participant in an HGF consortium with SciFlow and thus offers extended support and training. SciFlow is aimed at anyone who wants to work on a document with several people, but primarily at scientists. These can automatically format the text for the intended journal using templates, and their own reference management systems can be integrated. Furthermore, reports, meeting notes and data management plans can also be created with SciFlow.
The already existing templates can be found in SciFlow-portal for HZI: https://sciflow.net/hzi
(More general scientific templates for scientific reports, grant applications etc. will soon be available in the SciFlow(HZI) portal in a separate section, currently there are some general templates in the section "Haus- und Abschlussarbeiten/”(term papers and theses) and the templates Meeting minutes (de, en), report (de), Data management plan (Horizon 2020, DFG, BMBF)
Get to know SciFlow in this SciFlow-webinars:
4.11.2021 (Thursday), 10-11 a.m. incl. new features change tracking & spell check, recording https://us02web.zoom.us/webinar/register/WN_67AIzacPTz-yFoT1VFP-fA
- 27. Apr. 2021, 10-11 a.m German incl. new features, recording link on Intrane-page "SciFlow"
- 4. May 2021, 10-11 a.m., English, incl. new features, recording link on Intrane-page "SciFlow"
- 22. Sept. 2020, 10-11 a.m., German, see Vortragsankündigung-notification resp. Intranet-Newsposting for registration-link
Demo (©OVGU): SciFlow- kollaboratives Wissenschaftl. Arbeiten /SciFlow-connecting scientific writers
- Online text editor (similar to GoogleDocs, but DSGVO compliant and secure) with image, formula and citation integration
- Cooperation with any number of authors (also outside the institution) possible
- Formatting and export via templates at the end of the writing process for texts formatted ready for submission (to include comments into the export enter "comments" in the template search)
- Involvement of the literature administrations Zotero, Mendeley and BibTex (Citavi is in work, a HGF consortium will work for the integration of RIS/EndNote).
- Since the use of the basic system is free of charge for everyone, you can also work and write with colleagues outside the HGF without any problems.
- The servers are located in Germany (DSGVO compliant); SciFlow is a start-up from Magdeburg.
- Still missing journal templates will be created free of charge for licensing institutes (after checking the Journal-list in SciFlow(HZI)-Portal via Button „Template anfragen“) within 2-3 weeks, without a license agreement only via individual invoice fee.
PS: Similar tools like Authorea or Overleaf are much more expensive as institutional version and come from the Anglo-American area, so they are not DSGVO-compliant. The FZ Jülich looked at all 3 tools and came to the conclusion that only SciFlow is DSGVO-compliant and thus institutionally licensable.
FigShare, Dryad Digital Repository, Zenodo & Co. (Research Data Repositories/ Forschungsdaten-Repositorien)
Research data (opt-in) as well as the publications (an obligation) ought to be disclosed according to the rules of funding organizations like Horizon2020 (more details on our page "OpenAccess"). For depositing research data several repositories exist:
- discipline-specific or subject-specific repositories (e.g. Genbank)
- Figshare (www.figshare.com) is an online digital repository of research data (digital data, figures, images, videos, etc.). The company allows data citation and the connection to your personal researcher-ID via ORCID (see figshare's infos on ORCID).
- Dryad Digital Repository (www.datadryad.org) is an online repository containing the data underlying scientific publications. Data in Dryad are assigned a unique object identifier (DOI) to allow data citations. Dryad is governed by a non-profit membership organisation. Membership is open to stakeholder organisations such as journals, scientific societies, publishers, research institutions and funding organisations.
- ZENODO (http://zenodo.org) which is the former OpenAIRE 'Orphan Repository' - now hosted by CERN - is a repository that accepts both publications and datasets (see Zenodo FAQ: http://zenodo.org/faq).
- institutional platform service: RADAR (more details on intranet-page RADAR):
The ReseArch DAta Repository (RADAR) is a cross-disciplinary data archive for the publication and archiving of research data. This data typically derives from academic/scientific studies and completed projects. This ensures the traceability, reproducibility and transparency of research results while heightening the visibility of research data through independent publication. Additionally, the published data can be used to address new research questions.
RADAR-Portal (details): https://radar.products.fiz-karlsruhe.de/de/radarabout/ueber-radar
RADAR-Login (for registered HZI members): https://www.radar-service.eu/radar-backend/login-page
Preprint-Server (arxiv, bioRxiv & Co.) & Preprint-Suchmaschine (search.bioPreprint)
Preprint server enable a direct and free delivery of new knowledge. Here you find some Preprint-Server listed (more details regarding Preprint-Server contains the Table "Preprint servers and general repositories accepting preprints" (DOI: http://dx.doi.org/10.7554/eLife.16800.003) of the paper "How open science helps researchers succeed" ):
- arxiv.org (funded by Cornell University Library, Simons Foundation and other institutions): reliable Preprint-Server, which since 1991 covers the disciplines of physics, mathematics, computer science, non-linear sciences, statistics, and quantitative biology - and has therefore been indispensable for over two decades
- bioRxiv.org (maintained by Cold Spring Harbor Laboratory): a repository for Biological Sciences which includes new, confirming or contradictory research results, ranging from animal behavior and perception to clinical trials, neurosciences, and zoology.
- F1000Research (member of Science Navigation Group): provides an open science platform for the immediate publication of scientific communication. The articles with the relevant research data are published within one week and are open for Open Peer Review and user comments (posters and slides receive a DOI / Digital Object Identifier (see above) and can be quoted immediately)
- PeerJPreprints: is the Preprint-Server of the peer-reviewed Open-Access-Journal of the Mega-journal PeerJ, which covers Biology, Life sciences, Medicine and Computer Science. Their goal is to reduce costs and, at the same time, to publish more efficient innovative research. Submissions are free of charge, may be submitted as a draft, incomplete or final version, and are generally available online within one day after the editorial permission.
- Zenodo: is a repository for research data that has also been used as a preprint repository because it provides a document preview and a DOI / Digital Object Identifier (see above).
- Table "Preprint servers and general repositories accepting preprints" (DOI: http://dx.doi.org/10.7554/eLife.16800.003) of the paper "How open science helps researchers succeed" )
- FAQ on Preprints (ZB Med, Publisso) / FAQ zu Preprints (ZB Med, Publisso)
Search engine for preprints: search.bioPreprint or PrePubMed
(See News-posting "Preprints : publish your papers and search for preprints of others via search.bioPreprint" of 28. July 2016 )
Statistical Analysis with graphical processing/ simulation software
When you reach the limits of MS Excel & Co., there are several tools that you can use:
- SigmaPlot (containing SigmaStat): this rather intuitive Software is available on each HZI-workstation in the Softwarecenter:
Start > All Programs > Microsoft Systems Center > Configuration Manager > Softwarecenter (described with Screenshots for Endnote: "Installation of Endnote")
- OriginPro (ca. 10 single licences) and GraphPatPrism (300€ per single licence) are used by some colleagues
- StatFingerprints: the program "StatFingerprints" runs on R and is a free program that provides an environment for statistical calculation and graphics creation (R development Core Team 2008). StatFingerprints user manual can be downloaded at http://cran.r-project.org/web/packages/StatFingerprints/index.html (see Michelland et al.: StatFingerprints : a friendly graphical interface program for processing and analysis of microbial fingerprint profiles )
VirusMapper is a high-throughput, open-source ImageJ plugin for single-particle analysis in fluorescence microscopy, particularly super-resolution microscopy. It provides a platform for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. VirusMapper uses naive averaging to create models of the distribution of particular labelled species within larger structures. - VirusMapper-Software (Download, Overview and Tutorials) - details contains the article "VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy." in Scientific Reports Report 6:2016 (DOI: 10.1038/srep29132)
- Medical Imaging Interaction Toolkit (MITK), created by mint medical and the German Cancer Research Center / Deutsches Krebsforschungszentrum (DKFZ) is a free open-source software system for development of interactive medical image processing software. Medical Imaging Interaction Toolkit (MITK) combines the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) with an application framework. As a toolkit, MITK offers those features that are relevant for the development of interactive medical imaging software covered neither by ITK nor VTK, see the Toolkit Features.
MITK can be used or integrated with existing solutions in several ways, see Research Platform for examples - for a description of how to use it see Tutorials.
Science tools for Research
Although you may have tools and resources for doing your research it might be good to look out for even better tools, e.g. via
- Medfloss.org provides a comprehensive and structured overview of Free/Libre and Open Source Software (FLOSS): you can search for software tools via the Project-Wizard -please read the Medfloss' Mission Statement for further details
- Tools during specific steps of scientific work cycle: Digital tools podcast OSR039 at OpenScienceRadio (only German)
- the Resource Identification Portal was created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in our system where more than one identifier exists for a single resource.- Directly search for Resources via facets (e.g. resource type, parent organization, organism etc.)
- Digital Research Tools (DiRT) - Directory: aimed to serve mainly digital humanists but also others conducting digital research to find and compare resources (e.g. content management systems, OCR, statistical analysis packages, mindmapping software)
- Online Bioinformatics Resource Collection (OBRC): developed by the University of Pittsburgh's Health Sciences Library System to discover databanks and bioinformatics software.
- ChemBioHub: From compound registration to managing general orders, the ChemBio Hub can help you get your laboratory organised: you can use ChemBioHub to manage everything from compounds, plasmids, cell structures to antibodies and mouse data (see details in ChemBioHub-Wiki). Addendum: ChemBioHub can also be used on mobile devices (App in GooglePlay und Apple)
When using an URL it might happen, that either the content/ layout has changed or the URL is too old to be accessible. Via wayback-machine of InternetArchive (hosted by archive.org) you can try to access the previous webpage/ URL respectively its former layout ( see Wayback-FAQ).
To ensure to have permanent access to a web resource make a snapshot via Internet Archive, cc and/ or weblock.io
Web2.0 in general
As so many new tools arise it is rather difficult to stay up-to-date. The Social Media Prisma is one of the most comprehensive collections. This collection of tools is updated regularly and is sorted by key functions.