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Software in TSD - Amnesia, Gitea, R, Stata, Perl, Python, SPSS and IGV

Third party software for use with TSD.

  
TSD support has limited time for each case. If needed, we can offer paid support.

Prices

See the TSD price list here.

Standard software in TSD

TSD runs on Windows Server 2019.

Standard software includes: 

  • PDF-reader
  • 7-zip
  • Kleopatra
  • PuTTy

Installing applications


Project administrators (i.e. members of the pxx-admin-group) can install applications from the Software Center, a self-service software management solution available on all Windows workstations. Everyone may use Software Center to see what software is available for installation, but only project administrators may install such software. To find the Software Center:

  • Click the Start button in the bottom left corner, and start typing Software Center:
    Windows 2019 Windows 2012
    Software Center in the Start Menu on Windows 2019 Software center in the Start Menu on Windows 2012

Then select Applications in the menu on the left and browse through available applications. You can use multi select mode when installing multiple applications:
 

Selecting multiple items with Software Center

Licensed software

Software UiO UH-sector 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

BYOL - Bring Your Own License - allows researchers to use software they have a license for in TSD.
 

Observe:

  • The license belongs to the researcher, not the project.
  • The researcher must acquire permission to use the license inside TSD. 

Installing and using R in TSD

You can use R and RStudio in TSD.

Help on usage, RStudio, package installation, etc.

Start SPSS in Windows

  1. Click Start.
    You'll find the button on the bottom left.

    Start button
  2. Click the arrow.

    arrow
  3. Click IBM SPSS Statistics 25.

    list of available software

Linux in TSD

TSD runs on the UiO version of the RedHat Enterprise Linux distribution. The following software is included:

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

Containers in TSD

You can use containers in the Linux version of TSD.

Read more about the use of containers here.

Sharing data and software between projects

The /shared folder is available to all members of all projects across TSD. All data and all software that might be of interest to everyone is available here. 

In the /shared folder you will find:

  • /shared/data/durable/bioinformatics/

    • ref/ contains public reference data

    • src/ contains source code for bioinformatics software 

    • lib/ contains a bioinformatics software library 

  • /shared/data/durable/comp_psyc

    • a variety of topics within the field of computational psychology

Data anonymization 

In cooperation with  EOSC-hub and OpenAIRE TSD supports data anonymization with Amnesia.
 
Amnesia is a flexible tool for anonymization that transforms relational and transactional databases for statistical analysis and removes all identifying information from sensitive data. Amnesia removes all directly identifiable data like names, SSNs and such, and changes secondary identifiers like birth rates and postal numbers so no one can be identified from the data.  Amnesia supports k-anonymity and km-anonymity.

TSD offers Amnesia on the Windows host. To get Amnesia in your TSD project, contact tsd-drift@usit.uio.no

Gitea - available software in TSD

Inside TSD you will find Gitea - a list of software developed and maintained by TSD projects. This might be useful to your project. TSD staff is not available for support and maintenance of Gitea software. Please contact the developer directly.

Other available software

Follow the links for user manuals:

Requests for other software

Our infrastucture is our number one priority. Any request for other software will be risk assessed. 

Installation of other software takes from one day to four weeks depending on the complexity of the package and changes necessary to support it. You might have to pay for the time required.

  1. Extra software on Windows in TSD:
    Mail tsd-drift@usit.uio.no

  2. Extra software on Linux OS in TSD (Dockers containers included) or Colossus:
    Fill in this request form

  3. Extra software on /share directory:
    Mail tsd-drift@usit.uio.no

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Published Aug. 23, 2021 2:33 PM - Last modified June 1, 2022 2:24 PM