Data · dataset · 2024
Onco* version 0.1.0
Listed in DaRUS
Onco* version 0.1.0 Onco* is a module based umbrella software project for numerical simulations of patient-specific cancer diseases, see following figure.
Description
From given input states of medical images the disease is modelled and its evolution is simulated giving possible predictions. In this way, a digital cancer patient is created, which could be used as a basis for further research, as a decision-making tool for doctors in diagnosis and treatment and as an additional illustrative demonstrator for enabling patients understand their individual disease.
All parts resolve to an open-access framework, that is ment to be an accelerator for the digital cancer patient. Each module can be installed and run independently. The current state of development comprises the following modules: OncoFEM OncoGEN OncoTUM OncoSTR Content The uploaded virtual box is a virtual machine of a linux mint 21.2 cinnamon, 64 bit system and 8 GB RAM.
Read the rest (3 more)
The machine contains the pre-installed version of OncoFEM version 1.0, that corresponds to its related publication. The virtual machine need to be imported in Oracle VM VirtualBox. Username: onco password: 0000 The pre-installed version of onco* is implemented in a conda environment that is activated with the terminal command $conda activate oncofem The Software can be found in /home/ with the sub-folder for the tutorials, that can be run with $python3 oncofem_tut_01_quick_start Of course, the tutorials will only run, if the system meets the necessary requirements.
The tutorials (1, 2, 3, 4, 5, 6) where performed on a local machine (intel cpu i7-9700k with 3.6 GHz, 128 GB RAM). The tumor segmentation (tutorial 7, 8) have been tested on a different machine with a gpu (Nvidia a40, 48 GB VRAM, 32 core AMD epyc type 7452). For testing, the discretisation in space is decreased, compared to the results published in the respective paper.
This is the software state at version 0.1.0 and the actual development can be found in the respective github. OncoFEM OncoGEN OncoTUM OncoSTR
Links
Where it is published
- Dataverse dataset page darus.uni-stuttgart.de/dataset.xhtml?persistentId=doi%3A10.18419%2FDARUS-4651 ↗
landing page · from darus uni stuttgart de
- DOI doi.org/10.18419/darus-4651 ↗
DOI / persistent id · from darus uni stuttgart de
Catalogue records · 1
- Dataverse API darus.uni-stuttgart.de/api/datasets/:persistentId/?persistentId=doi%3A10.18419%2FDARU… ↗
metadata API · from darus uni stuttgart de
Topics
- Stated by source
- Engineering
- From keywords
- Cancer · Engineering · Simulation
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DaRUS | doi:10.18419/DARUS-4651 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[disease].local:disease:cancer | mapping · darus uni stuttgart de | vocabulary-mapper@1.0.0 | keywords['Tumor'] |
| concepts[disease].local:disease:disease | enrichment · darus uni stuttgart de | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].dataverse_subject:engineering | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[method].local:method:simulation | mapping · darus uni stuttgart de | vocabulary-mapper@1.0.0 | keywords['Simulation'] |
| concepts[modality].local:modality:image | enrichment · darus uni stuttgart de | keyword-concept-rules@1.0.0 | title+description (65%) |
| created_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| description | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /description |
| publication_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| title | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /name |
| updated_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| version_label | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 |