Electronic Laboratory Notebook: Organize Your Research Quickly & Efficiently

1. Electronic Laboratory Notebook: Organize Your Research Quickly & Efficiently Yannick Pouliot, PhD Bioresearch Informationist Lane Medical Library & Knowledge Management Center 8/19/2008

2. The Bioresearch Informationist: At Your Service • Yannick Pouliot, PhD, Lane Medical Library & Knowledge Management Center • Bioresearch Informationist≈ computational biologist in residence • Lane Library service • Closely coordinated with CMGM • Role: Support laboratory researchers regarding biocomputational resources and their use • …especially postdocs Contact:lanebioresearch@stanford.edu 2

3. Goal Survey the CambridgeSoft’s electronic laboratory notebook • … and associated issues 3

4. Disclaimer This is all new to us, such that “Stanford” has limited experience with E-Notebook 4

5. Laboratory Notebooks: General Considerations 5

6. Signatures and Witnesses • To be legally valid regarding intellectual property, lab notebooks need to be: • Signed and dated by you • Countersigned and dated by a witness • Witness = person who will not be named as a co-inventor and who is not working on the project • “At least one other investigator, not a co-worker or joint inventor, should regularly look over the entries and witness the same by applying his signature and date.” • Stanford Office of Technology Licensing • Notebook pages need regular ongoing signing, e.g., once a week • E-Notebook has built-in reminders about Notebooks or pages that have been open too long, or have not been signed off within an acceptable time period. • E-Notebook supports both paper and electronic witnessing: • Paper-based method: pages are printed, signed, and countersigned as with a regular paper notebook. • Electronic method: a PDF document of the electronically signed and witnessed page is kept in a separate archive. 6

7. Why Electronic Lab Notebooks? • Easy to read entries • Easy to enter data: typing, pasting, direct transfer • Easy to search for entries, and not just text searching… • Easy to backup • real handy, especially when leaving Stanford • Reminder: all lab notebooks are STANFORD PROPERTY → physical copying required. 7

8. Important Considerations • Using an ELN is a commitment • You’re getting married… • Will use of E-Notebook become a problem for lab mates or collaborators? • Actually, it can greatly facilitate collaborations… • You must be a Stanford affiliate to use software • Software requires yearly key update to continue working 8

9. So What has Stanford Licensed? • Swain Chemistry and Chemical Engineering Library has purchased site license for complete ChemBioOffice Ultra 2008suite • ChemBioOffice Ultra 2008 = Collection of powerful chemistry-oriented programs • Windows only… • Two suite components with applicability to bioresearch: • E-Notebook: really a general purpose lab notebook… • BioAssay Manager • E-Notebook is part of suite • Stanford has licensed personal version only → everything runs locally • Other version include Enterprise and Workgroup • Installation instructions here: http://lane.stanford.edu/howto/index.html?id=_3470 9

10. E-Notebook Features and Issues 10

11. What is E-Notebook? • E-Notebook = locally installed program, Windows-only • All data are stored in a MS SQL Server database • → very secure, good backup tools • Users can interact with database directly • Personal version of E-Notebook relies on SQL Server free version → 4 GByte max • If more needed, you can purchase your own SQL Server license → unlimited storage, not expensive for academics Important: Use of SQL Server means you must be administrator of the machine on which E-Notebook is to be installed! 11

12. E-Notebook: Major Features • Highly configurable lab journal with “pages” populated from • ChemDraw • Microsoft Office: Word, Excel, PowerPoint • Spectral software • Major features: • Text searching • Searching by compound structure and properties • Ability to draw reactions in ChemDraw • Ability to perform stoichiometric calculations • Complete audit trail of experiments at each save, including username and timestamp • Can use preexisting protocols to automatically add data from experiments using AutoText 12

13. An E-Notebook Strong Point: Integration with MS Office • E-Notebook works with MS Office2003 programs running on Win XP or Vista: • Word • Excel • PowerPoint • MS Office 2007 will be supported … next year • Reminder: All E-Notebook data remain in database → nothing saved in file system 13

14. E-Notebook Supports Native Format Analytical Data • Can import of LC/MS, NMR, IR, and other forms of raw analytical data directly from: • ACD/Labs SpecX • Thermo Galactic GRAMS • Waters NuGenesis • Agilent CyberLAB → direct access to external databases also available • Output from analytical instrument workstations can also be imported as graphical images • Oddly enough, every image format is supported EXCEPT tif… (?) 14

15. Searching Notebook Entries Different forms of searching supported: • Text searching • Extremely powerful chemistry searching capabilities: • Differentiates between reactants and products • Supports chirality • Supports rich atom and bond type definitions. • Mixed field searches supported • E.g., combining structural and text/numeric queries: Return all instances of a given structure with a property of X and value greater than Y → Queries and their results may be saved for later re-use 15

16. Managing Experimental Protocols • Experiments can be tightly associated with their protocol, thanks to the notion of a “page” • A page can have lots of sections, one which contains a protocol • Beyond pure text, protocols may be associated with an E-Notebook in several ways: • Forms which embed the protocol itself • The linking of forms to external data sources which store the protocol (non-local protocol). • Forms may also be automatically populated by data retrieved from external databases 16

17. E-Notebook Supports Direct Data Acquisition • Forms can be created to capture of data from any type of experiment. • Populating forms can be achieved by… • Manually entering data into a form’s fields • Importing data from externally generated tabular data such as Excel • Automatically transferring data via a programmatic interface • Common data types include: • Real and integer numbers • Text • Tables • Molecular structures • Images 17

18. Forms can be used to ensure that correct results are being captured Within a form, check-offs can be included at each step of a process, e.g.: • Boundary checking • no reaction yields >100%... • Type checking • can only select “μg”, not “mg” • Field checking: requiring all fields to be filled 18

19. Intellectual Property Protection E-Notebook provides extremely robust auditing capabilities: • When a page is created/saved/printed/changed, a record of that action is kept in the database. • A complete audit trail is part of the final printed record. • Earlier versions of pages may be easily recalled and compared to the current version. • The Notebook may be configured to link change pages or continuation pages to another page once it has been closed. 19

20. Reporting Capabilities E-Notebook provides excellent ability to understand one’s research globally, e.g.: • Number of experiments involved a given gene • Kinds of experiments were performed on a given gene • What hosts were used to produce a vector • What mouse strains where selected as transgene recipients • Queries can be saved for future use • … and in fact shared with others… 20

21. Further Important Considerations 21

22. The Importance of (Proper) Backups • Computers fail… • 1% chance of having hard disk failure in first year of operation… • HD failure = loosing/damaging physical lab notebook → Advantage: backing-up is easy and cheap • Backing up to an external hard disk is good… • But not ideal if the disk is next to your computer… → Solution: Copy backup file to e.g. MS SkyDrive for off-site storage • Back up approaches: • Exporting to MS Word or Adobe PDF • Exporting database in XML format • Exporting database using E-Notebook’s Administrator tool 22

23. More Questions You Might Have • Backward compatibility of newer versions of e-Notebook? → CambridgeSoft specifically tests to ensure full compatible with prior versions of e-Notebook • → if you upgrade, you’ll be able to import into current version • What if you leave Stanford? • You or your institution can provide a key to your existing software, which will become unusable within a year. 23

24. Questions? 24