SMIR supports now the upload of
- GSM – Genomic Sample
- GSE – Genomic Series
- GPL – Genomic Platform
in the MINiML (xml) format
MINiML (MIAME Notation in Markup Language, pronounced ‘minimal’) is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relations between objects: Platform (e.g., array), Sample (e.g., hybridization), and Series (experiment). MINiML captures all components of the MIAME checklist, as well as any additional information that the submitter wants to provide. MINiML uses XML Schema as syntax.
The statismo developers have added a command line interface to Statismo and they have released version 0.11.0!
It is now possible to perform the most common shape modelling tasks directly from the command line withou any programming involved.
The initial set of command line features include tools
- for model building
- for exploring a model
- for fitting a model to surfaces and images.
You will find the full list of currently available tools as well as two common use case scenarios on the statismo wiki.
Head over to github to download the statismo CLI or to give feedback to the devs!
A Special thanks goes to Frank Mueller from the University of Basel who developed the initial toolset.
The VSD-SMIR has received support for an additional Dataformat! The CDISC-ODM standard has been included to store Clinical Trial Data. You can now manage Clinical Research Form information together with imaging and precessed data on the VSD-SMIR.
“The CDISC Operational Data Model (ODM), which is maintained by the CDISC XML Technologies Team, is designed to facilitate the regulatory-compliant acquisition, archive and interchange of metadata and data for clinical research studies. ODM is a vendor neutral, platform independent format for interchange and archive of clinical study data … “. CDISC-ODM website