Software

TSD servers has a number of software packages installed by default and optional packages are available with the possibility to make additional requests for software.

Windows

TSD is running Windows Server 2012 R2.

Standard software on the VMs include: 

  • MS Office (Word, Excel, etc.) There will be an additional license fee for users affiliated with an organisation with no site license agreement.
  • R (click link for package install info)
  • WWW browser (no access to the internet)
  • PDF-reader
  • 7zip
  • GPGA
  • Kleopatra
  • Encryption wizzard
  • PuTTy
  • Integrated Genome Viewer (IGV)
  • Python, java, Perl interpreters may be installed on request.

Optional add ons

HyperResearch and HyperTranscribe will not be available for UiO-users after 01.07.2018 (guidelines and reference to alternative software)

  • SAS
    • offered for free to University of Oslo (UiO) users as part of a site license agreement.
  • SPSS
  • STATA
    • STATA-SE and MP8 is available to UiO users at no additional cost
    • STATA-SE and MP8 is available to not-UiO users at no additional cost, if they belong to an institution having a valid equivalent site lisence
    • STATA MP8 is offered to non-UiO users for an additional fee. Current rate is NOK 3.000,- per year per external user in the project.
  • MatLab
    • offered for free to University of Oslo users as part of a site license agreement.
    • at the moment not available for external users due to cost.
  • NVivo Pro
    • offered for free to University of Oslo users as part of a site license agreement.
    • offered for free to persons affiliated to other educational institutions in Norway having a valid NVivo site license agreemnet. (UiT, NTNU, UiB, HiOA, etc..)
    • for other institutions (ex. university hospitals) we support a "bring-your-own-license" model. Contact tsd-contact@usit.uio.no for more info
    • not available for external single users due to cost.
  • RStudio
  • StatTransfer
    • offered for free to University of Oslo users as part of a site license agreement.
    • at the moment not available for external users due to cost.
  • f4transkript 
    • offered for free to University of Oslo users as part of a site license agreement.
    • at the moment not available for external users due to cost.
  • VLC media player
  • HandBrake

Linux

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

  • Libre Office (aka Open Office)
  • R
  • Emacs
  • WWW browser (no access to the internet)
  • Perl interpreter
  • Python interpreter
  • xdg-open
  • display
  • VLC media player

For installing additional Python packages please have a look at: http://www.uio.no/english/services/it/research/hpc/abel/help/software/Python%202.html

Installing R packages

For any additional software requests, please contact tsd-drift@usit.uio.no

Colossus software

The Colossus software portfolio is to a large extent identical to what is installed on the Abel cluster at University of Oslo, with the exemption of packages that are exclusively licensed to Abel. Please have a look at the Abel software page for a listing of available packages. Any requests for additional software on Colossus must be submitted via this form.

It is possible to use the software from the Colossus portfolio on the project linux VM, thus avoiding the cost of CPUs and storage on the Colossus cluster. Send a mail to tsd-drift@usit.uio.no to request the access to the modulefiles. Once the software is loaded as a module (module load <software-name>), it can be launched from the VM terminal. No job script is required.

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 made available to everyone. User contributions to this folder is very welcome and any requests may be directed to tsd-drift@usit.uio.no.

TSD support will attempt to provide items of general interest to this folder, while the helpdesk at Elixir.no will make contributions from the Bioinformatics domain.

Currently you will find:

  • /shared/data/durable/bioinformatics/

    • ref/  containing public referance 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

Request extra software

We try to accommodate your software requests as much as possible, in order to make your working space in TSD optimal for your research. 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

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"

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Published Nov. 9, 2017 9:56 AM - Last modified July 25, 2019 9:21 AM