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= [[SysLogics]] Portal = | = [[SysLogics]] Portal = | ||
* The [https://www.cebitec.uni-bielefeld.de/groups/brf/software/portal/portal/syslogics/ SysLogics Portal] can be used to manage sequence collections with SAMS or genome datasets with GenDB. In addition to a consistent sequence annotation, the expression data generated in [[SysLogics]] can be uploaded and viewed with ArrayLIMS and subsequently analyzed with [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA 2]. Metabolomics datasets can be uploaded, organized and analyzed using the [http:// | * The [https://www.cebitec.uni-bielefeld.de/groups/brf/software/portal/portal/syslogics/ SysLogics Portal] can be used to manage sequence collections with SAMS or genome datasets with GenDB. In addition to a consistent sequence annotation, the expression data generated in [[SysLogics]] can be uploaded and viewed with ArrayLIMS and subsequently analyzed with [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA 2]. Metabolomics datasets can be uploaded, organized and analyzed using the [http://meltdb.cebitec.uni-bielefeld.de MeltDB] platform. Support for quantitative proteomics is available via [http://qupe.cebitec.uni-bielefeld.de QuPE]. | ||
== Metabolomics and Proteomics == | == Metabolomics and Proteomics == | ||
The focus of the QuPE and MeltDB systems is the quantitative analysis and integration of functional genomics data. | |||
Both systems support open and standardized file formats from mass spectrometry based analysis. | |||
* [http://www.unidata.ucar.edu/netcdf netCDF (AIA/ANDI MS)] | * [http://www.unidata.ucar.edu/netcdf netCDF (AIA/ANDI MS)] | ||
* [http://www.ncbi.nlm.nih.gov/pubmed/15529173 mzXML] | * [http://www.ncbi.nlm.nih.gov/pubmed/15529173 mzXML] | ||
* [http://www.ncbi.nlm.nih.gov/pubmed/17907277 mzData] | * [http://www.ncbi.nlm.nih.gov/pubmed/17907277 mzData] | ||
* [http://www.ncbi.nlm.nih.gov/pubmed/20716697 mzML] | |||
An overview of various conversion tools for these formats can be found [http://en.wikipedia.org/wiki/Mass_spectrometry_data_formats here] | |||
== Transcriptomics == | == Transcriptomics == | ||
The recently released [http://www.biomedcentral.com/1471-2105/10/50 EMMA 2] system supports a variety of micro array data standards. The system supports the upload of array data using the Imagene or Genepix software formats as well as general comma or tab-separated files and CEL-files. For [[NimbleGen]] arrays, pair files containing pairwise probe intensities are imported. Due to the modular architecture of the importer, new formats can be added easily. | |||
Latest revision as of 14:35, 23 February 2012
SysLogics Portal
- The SysLogics Portal can be used to manage sequence collections with SAMS or genome datasets with GenDB. In addition to a consistent sequence annotation, the expression data generated in SysLogics can be uploaded and viewed with ArrayLIMS and subsequently analyzed with EMMA 2. Metabolomics datasets can be uploaded, organized and analyzed using the MeltDB platform. Support for quantitative proteomics is available via QuPE.
Metabolomics and Proteomics
The focus of the QuPE and MeltDB systems is the quantitative analysis and integration of functional genomics data. Both systems support open and standardized file formats from mass spectrometry based analysis.
An overview of various conversion tools for these formats can be found here
Transcriptomics
The recently released EMMA 2 system supports a variety of micro array data standards. The system supports the upload of array data using the Imagene or Genepix software formats as well as general comma or tab-separated files and CEL-files. For NimbleGen arrays, pair files containing pairwise probe intensities are imported. Due to the modular architecture of the importer, new formats can be added easily.