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Additional Science-Tools

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.

 

Access eJournals incl. access details via EZB/ Elektronic Journals' Library:

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.

Example-of-Article-Plagiarism-Diagram (CC3.0, adapted from Carrot Lord)

 

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:

 

DFN-Terminplaner für Terminkoordination (https://terminplaner2.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

 

DOI-Resolver (http://dx.doi.org/):

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.

 

oaDOI-Resolver (https://oadoi.org), now Unpaywall (http://unpaywall.org/) :

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 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)

 

Further information:

 

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).

 

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).

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)

     

    Wayback-Machine

    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.