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

2. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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 CMGMCMGM Role: Support laboratory researchers regarding biocomputational resources and their use …especially postdocs Contact: lanebioresearch@stanford.edulanebioresearch@stanford.edu

3. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 3 Goal Survey the CambridgeSoft’s electronic laboratory notebook  … and associated issues

4. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 4 Disclaimer This is all new to us, such that “Stanford” has limited experience with E-Notebook

5. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 5 Laboratory Notebooks: General Considerations

6. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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 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.

7. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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.

8. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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

9. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 9 So What has Stanford Licensed? Swain Chemistry and Chemical Engineering Library has purchased site license for complete ChemBioOffice Ultra 2008 suite Swain Chemistry and Chemical Engineering Library suite 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 http://lane.stanford.edu/howto/index.html?id=_3470

10. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 10 E-Notebook Features and Issues

11. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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!

12. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 12 E-NotebookE-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

13. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 13 An E-Notebook Strong Point: Integration with MS Office E-Notebook works with MS Office 2003 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

14. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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… (?)

15. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 15 Searching Notebook Entries Different forms of searching supported: 1. Text searching 2. 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

16. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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: 1. Forms which embed the protocol itself 2. 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

17. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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

18. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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

19. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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.

20. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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…

21. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 21 Further Important Considerations

22. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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 storageMS SkyDrive Back up approaches: 1. Exporting to MS Word or Adobe PDF 2. Exporting database in XML format 3. Exporting database using E-Notebook’s Administrator tool

23. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 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.

24. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 24 Questions?