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Getting organizedValérie de Crécy-Lagard, [email protected]
Good record keeping (e.g. lab notebooks, best solutions to organize chemical inventory and strains)
How to handle large data sets
http://www.benchfly.com/blog/how-to-keep-a-lab-notebook/
How to organize data? Every field is impacted?
https://www.economist.com/printedition/2010-02-27
FAIR: Findable, Accessible, Interoperable, Reusable.
http://scholar.harvard.edu/files/mercecrosas/files/sdata201618.pdf
http://cms.uflib.ufl.edu/datamgmt/index
UF Libraries : good resources
UF Libraries: good place to start
http://guides.uflib.ufl.edu/c.php?g=147756&p=966316
In the cloud @UF
For Faculty and Staff not student1TB limit
https://it.ufl.edu/services/search/gatorcloud
For Faculty, Staff, Student
High Performance computing (HPC)@UF
https://help.rc.ufl.edu/doc/Getting_Started
Create Your local Lab Drive
• Set up by PI or Key Personnel/ Lab Manager• Every Lab Member has folder • Courtesy rules on creating and changing folders or
specific read-only permissions
Data types
• Research Notebooks• Inventories and ordering : consumables and
chemicals • Specialized collections: strains, plasmids,
oligonucleotides etc• Datasets: RNAseq, Field Studies, Proteomics,
Metabolomics, SNP data, etc etc….
Data types
• Research Notebooks• Inventories and ordering : consumables and
chemicals • Specialized collections: strains, plasmids,
oligonucleotides etc• Experimental datasets: RNAseq, Field Studies,
Proteomics, Metabolomics, SNP data, etc etc….• Other: Code, models
Electronic notebook (ELN): general solutions• http://campusguides.lib.utah.edu/ELNs
• Evernote/OneNote ( UF license)
• Open Science Framework OSF
Electronic notebook (ELN): general solutions OneNote example
Electronic notebook (ELN): general solutions OneNote example
Electronic notebook (ELN): lab specific solutions• http://campusguides.lib.utah.edu/ELNs
https://intercom.help/benchling
Data types
• Research Notebooks• Inventories and ordering : consumables and
chemicals • Specialized collections: strains, plasmids,
oligonucleotides etc• Experimental datasets: RNAseq, Field Studies,
Proteomics, Metabolomics, SNP data, etc etc….• Other: Code, models
Chemical inventories: New PI assistance
UF Chemical Inventories : Navigating ChemTracker
The website has detailed links to tutorials and guides in navigating around ChemTracker
Inventories and ordering : consumables and chemicals
Go to the request tab
Enter information on the item (vendor,
catalog number, price, URL, etc)
QUARTZY scans for better pricing on the
item
Accept quote and purchase
through QUARTZY
Reject quote and purchase item
externally or through MyUFMarket
QUARTZY features an Inventory comparable to ChemTracker.
Collection Databases
• Create your own : SQL http://sqlitebrowser.org/http://www.datacarpentry.org/sql-ecology-lesson/• Use ELN tools (Benchling has specific tools for
strain, plasmid databases)
Data types
• Research Notebooks• Inventories and ordering : consumables and
chemicals • Specialized collections: strains, plasmids,
oligonucleotides etc• Experimental datasets: RNAseq, Field Studies,
Proteomics, Metabolomics, SNP data, etc etc….• Other: Code, models
Best practices for reproduceabledata science• For every Project create Folder with Data/Input/
output/ code/ subfolders• Always add README TEXT file to explain ( should
be read before accessing data• Never change the initial data • Tools to insure traceability of changes with tools
such as such as githttp://swcarpentry.github.io/git-novice/
Deposit data to make it available with doi• https://dataverse.org
• https://figshare.com
Data types
• Research Notebooks• Inventories and ordering : consumables and
chemicals • Specialized collections: strains, plasmids,
oligonucleotides etc• Experimental datasets: RNAseq, Field Studies,
Proteomics, Metabolomics, SNP data, etc etc….• Other: Code, models
Depositit Codes and models
• Gitlab or Github (very general)- https://about.gitlab.com/ (private by default)- https://github.com/• Kbase ( more specialized)- https://kbase.us/
Data management plan tools @UF
DMP training
http://ufdc.ufl.edu/AA00014835/00087 http://ufdc.ufl.edu/AA00014835/00100
DMP resources at other libraries
https://library.stanford.edu/research/data-management-services/data-management-plans
https://software-carpentry.org/lessons/
http://www.datacarpentry.org/
Local Carpentry resource
https://github.com/UF-Carpentry/Coordination/wiki
HPC and Galaxy training at UF https://www.rc.ufl.edu/services/
Special Thanks to
• Crecy Lab members• Dr. Chris Reisch• Dr. Jo Marie Bacusmo• Dr. Geraldine Klarenberg