The Galaxy Team in Freiburg has a new member.
Fabio Cumbo is a PhD Candidate in Software Engineering at the University of Roma Tre in Rome, Italy. Previously member of the US Team of Galaxy, he has recently joined the Galaxy Team in Freiburg as a visiting scientist.
He is currently working on a tool that allow to rapidly identify all publicly available sequenced samples which express a particular transcript. The main idea under the realization of this tool is widely described in https://doi.org/10.1038/nbt.3442 and https://doi.org/10.1101/090464. This tool, in collaboration with the Nekrutenko Lab and Medvedev Lab at the Biochemistry and Molecular Biology Department of the Pennsylvania State University located in State College, PA, USA, is currently under construction and will be available pretty soon on the official Galaxy Toolshed under the name btman (BloomTree Manager).
He is also working on the integration of new Data Source Tools as the GDCWebApp service for the automatic extraction, extension, and conversion of all genomic and clinical data from the Genomic Data Commons portal. This web service is also able to filter out the experiments that respect some user defined rules on clinical and biospecimen information. The requested data can be finally converted in BED, GTF, CSV, and JSON format and directly sent to Galaxy as list of data collections. This data source tool is currently available on the Toolshed under the name gdcwebapp.
He will additionally work on the integration of the RNACentral portal as a new Data Source Tool.
Welcome Fabio Cumbo!