Tuma (finnish word for Nucleus) computing server is meant for an interactive computing workloads. In addition to the traditional SSH terminal access the server provides graphical desktop environment that can be used with the Remote Desktop Connection Protocol.
Server address: tuma.uef.fi
Server is connected to the storage space provided by the UEF IT Services for Research. More information can be found from the dedicated page.
All the available reference data sets are provided as-is. They are unmodified copies of the original files.
URL: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Following reference genomes can be found from the /apps/genomes/iGenomes folder.
| Home sapiens | Version |
|---|---|
| GRCh37 | Ensembl |
| GRCh38 | NCBI |
| GRCh38Decoy | NCBI |
| hg19 | UCSC |
| hg39 | UCSC |
| Mus musculus | Version |
|---|---|
| mm9 | UCSC |
| mm10 | UCSC |
| Rattus norvegicus | Version |
|---|---|
| rn4 | UCSC |
URL: https://gnomad.broadinstitute.org/downloads
Following variants can be found from the /research/groups/bioinformaticians/gnomAD-hg19-r2.1.1 folder.
| Data set | Version |
|---|---|
| Exome variants (.vcf.bgz, tbi) | gnomAD 2.1.1 / hg19 |
| Exome calling regions (.interval list) | gnomAD 2.1.1 / hg19 |
| Genome variants (.vcf.bgz, tbi) | gnomAD 2.1.1 / hg19 |
| Genome calling regions (.interval list) | gnomAD 2.1.1 / hg19 |
| Structural variants (.vcf.gz, tbi) | gnomAD 2.1.1 / hg19 |
System provides various graphical and terminal applications for the researchers.
Additionally to browser, office-suite and text editors the following graphical applications are available:
| Graphical Applications | Version |
|---|---|
| MATLAB | R2020b |
| RStudio | 3.6.3 |
| RStudio | 4.1.0 |
| Other Applications | Version | Address |
|---|---|---|
| Rstudio-Server | 4.1.0 | https://tuma.uef.fi/rstudio |
| Singularity Container |
To see the list of terminal application visit the available applications web page.