Tools and Work Aids Open Source Software at the University of Bern

Open Source

Short-URL to this site: www.opensource.unibe.ch

Open Source Software (OSS) are programs that are published under an Open Source license. This license allows OSS to be copied arbitrarily and the source code to be openly available and also to be modified. Thus OSS is always free of license costs and can be viewed transparently. OSS is particularly suitable for studies because there are many free programs that are useful for students. On this website, numerous recommendations, background information and tools are available to facilitate the use of OSS in studies at the University of Bern. However, it should be noted that due to the large number of OSS products, no end-user support for students can be provided.

Contact

The Research Center for Digital Sustainability, the support center for ICT-supported teaching and research as well as the university libraries will assist you in finding a suitable open source software for your needs. Please contact the teams or contact persons listed on the detail pages.

Information on OSS at other universities

Information on OSS is also available to students and staff at other Swiss universities:

Further information sources about Open Source

  • OSS Directory: Directory of Open Source Software companies, solutions and references
  • Open Source Study Switzerland 2015: Current figures on Open Source usage in Switzerland as well as technical articles and company profiles
  • /ch/open: Swiss Association for the Promotion of Open Source Software (membership for students: CHF 20 per year)
  • ifrOSS: Institute for Legal Affairs of Free and Open Source Software

Further lists of Open Source applications

Definition of Open Source

The term Open Source Software was defined in 1998 by the Open Source Initiative on the basis of 10 characteristics that all so-called open source licenses must comply with:

  1. Free Redistribution: The license shall not restrict any party from selling or giving away the software as a component of an aggregate software distribution containing programs from several different sources. The license shall not require a royalty or other fee for such sale.
  2. Source Code: The program must include source code, and must allow distribution in source code as well as compiled form. Where some form of a product is not distributed with source code, there must be a well-publicized means of obtaining the source code for no more than a reasonable reproduction cost preferably, downloading via the Internet without charge. The source code must be the preferred form in which a programmer would modify the program. Deliberately obfuscated source code is not allowed. Intermediate forms such as the output of a preprocessor or translator are not allowed.
  3. Derived Works: The license must allow modifications and derived works, and must allow them to be distributed under the same terms as the license of the original software.
  4. Integrity of The Author's Source Code: The license may restrict source-code from being distributed in modified form only if the license allows the distribution of "patch files" with the source code for the purpose of modifying the program at build time. The license must explicitly permit distribution of software built from modified source code. The license may require derived works to carry a different name or version number from the original software.
  5. No Discrimination Against Persons or Groups: The license must not discriminate against any person or group of persons.
  6. No Discrimination Against Fields of Endeavor: The license must not restrict anyone from making use of the program in a specific field of endeavor. For example, it may not restrict the program from being used in a business, or from being used for genetic research.
  7. Distribution of License: The rights attached to the program must apply to all to whom the program is redistributed without the need for execution of an additional license by those parties.
  8. License Must Not Be Specific to a Product: The rights attached to the program must not depend on the program's being part of a particular software distribution. If the program is extracted from that distribution and used or distributed within the terms of the program's license, all parties to whom the program is redistributed should have the same rights as those that are granted in conjunction with the original software distribution.
  9. License Must Not Restrict Other Software: The license must not place restrictions on other software that is distributed along with the licensed software. For example, the license must not insist that all other programs distributed on the same medium must be open-source software.
  10. License Must Be Technology-Neutral: No provision of the license may be predicated on any individual technology or style of interface.

Office

LibreOffice

LibreOffice is an open-source office package, which can hold a candle to the paid Microsoft Office package. The package contains a compilation of common tools for word processing, spreadsheets, presentation and drawing creation. A database management system and a formula editor are also included.

For university use, the LibreOffice Writer (the counterpart to Microsoft Office Word) is particularly noteworthy. This tool can do everything that Word can do, but in addition it contains a clearer administration of the format templates and a literature administration, which can be adapted to individual needs.

ProjectLibre

ProjectLibre is an open source project management software. Visually and functionally ProjectLibre imitates the MS-Project software. The software contains functions for project management such as a project plan, Gantt charts and much more. As standalone software ProjectLibre runs on Windows, Apple and Linux.
To install the software on an "Ubuntu" - Linux, a few additional steps are necessary, which are well described e.g. at (https://ubuntu-mate.community/t/how-to-install-projectlibre-a-professional-grade-project-management-tool-on-ubuntu-mate/4650).

Scribus

To create flyers, brochures or magazines, desktop publishing software (DTP) such as Adobe InDesign can be used. A free open source alternative is Scribus. With Scribus, students can create professional print data, and along the way learn what is needed to do so.

For many years, Scribus has been growing in popularity as an open source variant, so I would like to use this Scribus guide to introduce the program in detail. Using a drinks menu as an example, I will create professional print data with you, because students often have to prepare print jobs themselves and send them to professional printers. Scribus gives all students access to a good tool which not only allows them to prepare a correctly prepared print job, but also allows them to learn how to do it.

Literature Administration

BibDesk

BibDesk is a reference management program for Mac OS X. BibDesk uses the BibTeX format and is therefore particularly suitable for use with LaTeX.

Jabref

JabRef is a reference management program which uses the BibTeX format and is therefore ideally used in combination with LaTeX. JabRef is programmed in Java and runs under Microsoft Windows, Linux and Mac OS X.

Zotero

Zotero is a free, open source program for collecting, managing and citing bibliographic references. Zotero was originally developed as an extension for the Mozilla Firefox web browser and, with appropriate extensions, can still be used with Safari or Google Chrome. In combination with Microsoft Office Word and the LibreOffice Writer, however, the standalone desktop version in particular enables a very intuitive and fast way to manage literature for scientific texts.

Statistics

R

"R" is basically a free programming language with which you can perform all conceivable statistical calculations and evaluations. As a program package, "R" can be used on Linux, Mac and Windows and because it is part of a GNU project, it costs nothing. With the basic package it is possible to perform the most basic statistical calculations. The strength of "R" is the open and freely accessible programming language "S". This allows you to program additional packages that are tailored to your needs and calculate statistical procedures exactly the way you want. These possibilities have led to the fact that in the meantime additional packages exist for all conceivable calculation procedures.

Multimedia

Audacity

Free open source tool suitable for recording and audio editing. Audacity does not win any beauty contest, but impresses with its extensive functionality and the support of the following operating systems:  Windows, Mac OS X, GNU/Linux

VLC-Player

VLC is a free media player that can play practically all video and music files. Use the VLC player e.g. to play podcasts downloaded from ILIAS.

Medicine

Software for visualization and processing of medical images

The listed open source softwares are only for diagnostic support in teaching and research. They must not be used directly for the treatment and diagnosis of patients. 

Ginkgo CADx

Ginkgo CADx can convert a range of image formats JPEG, PNG, GIF, TIFF and PDF documents into DICOM files. The software has a DICOM viewer and working environment. Operating systems: Windows, Mac OS X, Linux.

ITK-SNAP

Interactive CC++ based software for segmentation of 3D structures. The user-friendly interface allows navigation in the 3D images and the display and measurement of individual anatomical regions. NIfTI and DICOM image formats are supported. The software is used in the following areas among others: Segmentation of the carotid artery, diffusion MRI (dMRI), prenatal image analysis, radiotherapy, orthodontics, brain morphometry.  Operating systems: Windows, Mac OS X, Linux.

Slicer

Software package for the analysis and visualization of images (incl. 4D). With the GUI interface interactive segmentations, surfaces and volumes can be displayed. Slicer can be used for image acquisition from MRI, CT, PET and microscopy. The website has a very good wiki with sample datasets. The version Slicer 4.4 now has an improved App Store to add plug-ins to Slicer.  Operating systems: Windows, Mac OS X, Linux.

Software to support the writing of systematic reviews and master theses

GATE

Leading toolkit for text mining, extraction of information (multilingual) and for word processing. Various document formats and databases can be used with GATE (TXT, HTML, XML, Doc, PDF, Java Serial, PostgreSQL, Lucene, Oracle). Operating systems: Windows, Mac OS X, Linux.

GRADEpro

Software to generate summary tables that meet the Cochrane standard. GRADEpro is available online for PC and Mac computers. For offline use an app can be downloaded in Google App.

OpenClinica

Software for finding and managing clinical research data, which is useful for setting up your own study. It is a web-based software accessible via a standard web browser.

Open Meta.Analyst (OMA)

OMA can be used to perform meta-analyses with binary, continuous or diagnostic data. The merging of the data is carried out using various "fixed" and "random-effects" methods (Bayesian, maximum likelihood analysis). The software can also be used to perform cumulative, subgroup or meta-regression analyses. Operating systems: Windows (64-bit only), Mac OS X.

RevMan

Review Manager (RevMan) is used to prepare high quality Cochrane reviews. Once the question has been formulated, the software can be used to draft the text, create tables and display the results. Meta-analyses and graphic presentations can be made with the software. Operating systems: Windows, Mac OS X, Linux.

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