Software

TSD servers has a number of software packages installed by default and optional packages are available upon request.

Windows

TSD is running Windows Server 2012 R2.

Standard software on the VMs include: 

  • MS Office
  • R
  • PDF-reader
  • 7zip
  • Kleopatra
  • PuTTy
  • Integrated Genome Viewer (IGV)

Licensed software

Software UiO UH Others
f4transkript Yes BYOL BYOL
IBM SPSS Yes BYOL BYOL
MATLAB Yes BYOL BYOL
NVivo Yes BYOL BYOL
SAS Yes BYOL BYOL
STATA Yes BYOL BYOL
StatTransfer Yes BYOL BYOL

The essence of the BYOL - 'Bring Your Own License' model in TSD is to facilitate researchers who have a valid license for a software approved by their Software Vendor. In such cases we can make that software available for the researcher in a TSD-project. This implies:

  • The license is per user and not per project.
  • The researcher takes the responsibility to contact the Software Vendor to get an approval to use her/his license key in a TSD-project.

How to start SPSS on Windows

  1. Click the Start button
    You can find this button in the lower-left corner of the screen.

  2. Click on the arrow

  3. Click on the "IBM SPSS Statistics 25"

Linux

TSD is running the UiO version of RHEL6 linux distribution,  that includes the following packages:

  • Libre Office
  • R
  • Emacs
  • Perl interpreter
  • Python interpreter
  • xdg-open
  • display
  • VLC media player
  • Installing R packages

Containers

Sharing data and software between projects

The /shared folder is readable by any user of any project in TSD. In this folder any data and/or software that may be of general interest is available.

In /shared folder, you will find:

  • /shared/data/durable/bioinformatics/

    • ref/  containing public reference data

    • src/ containing bioinformatics software source code

    • lib/ containing bioinformatics software libraries

  • /shared/data/durable/comp_psyc

    • miscellaneous from the domain of computational psychology

Data Anonymization 

As part of the collaboration with EOSC-hub and OpenAIRE projects, TSD supports data anonymization through Amnesia which is a flexible data anonymization tool that transforms relational and transactional databases to dataset where formal privacy guaranties hold. It allows to remove identifying information from sensitive data. Amnesia not only removes direct identifiers like names, SSNs etc but also transforms secondary identifiers like birth date and zip code so that individuals cannot be identified in the data. Amnesia supports k-anonymity and km-anonymity.

In TSD, Amnesia is offered on Windows hosts. To get Amnesia in your TSD project please contact tsd-drift@usit.uio.no

3rd party software

Here is a list of software, developed by TSD research projects, which may prove useful in your own TSD project. This is software developed and maintained by research projects, and TSD staff are not able to provide support or maintenance. If you decide to use this, and need help, the best course of action is to take contact with the maintainers directly.

Request for additional software

We try to accommodate your software requests as much as possible. However, since security is the primary concern for our infrastructure, only software approved by our IT-security officer will be installed.

The installation might take between one day up to four weeks, depending on the complexity of the software package and changes to the OS to support it. If the software installation requires many hours of experts work, we might request compensation before the installation activities.

  1. Extra software on the Windows OS virtual machines: Please send a request to tsd-drift@usit.uio.no

  2. Extra software on the Linux OS virtual machines (including Dockers containers): Please send a request to tsd-drift@usit.uio.no

  3. Extra software on Colossus: Any requests for additional software on Colossus must be submitted via this form.

  4. Extra software on /share: Please send a request to tsd-drift@usit.uio.no

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Published Nov. 9, 2017 9:56 AM - Last modified Oct. 20, 2020 12:48 PM