Getting organizedValérie de Crécy-Lagard, vcrecy@ufl.edu

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