This hands-on workshop will introduce the building blocks of the Python scripting environment. Participants will learn about basic programming concepts including simple and complex data types, conditionals and looping that are applicable to Python and other languages.
Making data publicly available is integral to the dissemination of research output. However, data submission to international repositories can be challenging. Identifying what metadata need to accompany data submissions, packaging data and metadata, and submitting large number of entries is complex and sometimes difficult for individual researchers.
Data chaperoning refers to the guidance and support provided by the EMBL-ABR:QCIF Node to help Australian researchers with the process of curating, formatting and managing research data for transfer to existing international data repositories, where it will be publicly accessible for reuse.
The QCIF Node team uses a range of scripts and standard operating procedures to support the submission of Australian genomics data to the European Nucleotide Archive (ENA), which is regularly synced with the NCBI Short Read Archive (SRA). Since early 2016, the EMBL-ABR: QCIF Node team has been working to further develop and support the data chaperoning service. This service is open to all Australian life science and medical researchers.
Data chaperoning services at the EMBL-ABR: QCIF Node
- Management of ENA data submission accounts accessible by researchers
- Data chaperoning helpdesk
- Submission of selected Bioplatforms Australia data to ENA
- Submission of researcher data to ENA
- Improvements to existing ENA data submission processes and infrastructure
- Broadening the range of supported datatypes
- Maintaining boutique data submission tools such as Tox|Note for venom-gland transcriptome data submission and toxin card creation on ArachnoServer.
Do you need Data Chaperoning help?
If you have genomics data to submit to ENA, and you’d like some help, please contact the Data Chaperoning service.
ENA allows 3 types of data submissions: sequencing reads, genome assemblies and assembled sequence and/or annotation. The Data Chaperoning service is working towards supporting other data types so feel free to contact us to ask for advice on other data types as well.
EMBL-ABR:QCIF Node Data Chaperoning team
||Nick Rhodes, QCIF Node
||Mike Thang, QCIF Node|
||Pierre Chaumeil, QCIF Node|
Other EMBL-ABR: QCIF Node team members are involved on-demand and according to the type of domain knowledge required.
Data Chaperoning Activity 2016