Transcript Electronic Laboratory Notebook: Organize Your Research

Electronic Laboratory
Notebook: Organize Your
Research Quickly & Efficiently
Yannick Pouliot, PhD
Bioresearch Informationist
Lane Medical Library & Knowledge Management Center
8/19/2008
Lane Medical Library & Knowledge Management Center
http://lane.stanford.edu
The Bioresearch Informationist: At Your Service
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Yannick Pouliot, PhD, Lane Medical Library &
Knowledge Management Center
Bioresearch Informationist ≈ computational biologist in
residence
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Lane Library service
Closely coordinated with CMGM
Role: Support laboratory researchers regarding
biocomputational resources and their use
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…especially postdocs
Contact: [email protected]
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
2
Goal
Survey the CambridgeSoft’s electronic
laboratory notebook
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… and associated issues
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
3
Disclaimer
This is all new to us, such that
“Stanford” has limited
experience with E-Notebook
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Laboratory Notebooks:
General Considerations
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Signatures and Witnesses
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To be legally valid regarding intellectual property, lab notebooks
need to be:
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Signed and dated by you
Countersigned and dated by a witness
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Witness = person who will not be named as a co-inventor and who
is not working on the project
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“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.”
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Notebook pages need regular ongoing signing, e.g., once a week
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Stanford Office of Technology Licensing
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:
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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.
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Why Electronic Lab Notebooks?
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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
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real handy, especially when leaving Stanford
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Reminder: all lab notebooks are STANFORD
PROPERTY → physical copying required.
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Important Considerations
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Using an ELN is a commitment
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You’re getting married…
Will use of E-Notebook become a problem for lab
mates or collaborators?
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Actually, it can greatly facilitate collaborations…
You must be a Stanford affiliate to use
software
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Software requires yearly key update to continue
working
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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So What has Stanford Licensed?
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Swain Chemistry and Chemical Engineering Library has
purchased site license for complete ChemBioOffice Ultra 2008
suite
ChemBioOffice Ultra 2008 = Collection of powerful chemistryoriented 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
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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E-Notebook Features and
Issues
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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What is E-Notebook?
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E-Notebook = locally installed program, Windowsonly
All data are stored in a MS SQL Server database
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→ 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
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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!
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
11
E-Notebook: Major Features
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Highly configurable lab journal with “pages” populated from
 ChemDraw
 Microsoft Office: Word, Excel, PowerPoint
 Spectral software
Major features:
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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
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Can use preexisting protocols to automatically add data from
experiments using AutoText
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
12
An E-Notebook Strong Point: Integration
with MS Office
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E-Notebook works with MS Office 2003
programs running on Win XP or Vista:
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Word
Excel
PowerPoint
MS Office 2007 will be supported … next
year
Reminder: All E-Notebook data remain in
database
→ nothing saved in file system
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
13
E-Notebook Supports Native Format
Analytical Data
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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
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Output from analytical instrument workstations can
also be imported as graphical images
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Oddly enough, every image format is supported EXCEPT
tif… (?)
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Searching Notebook Entries
Different forms of searching supported:
1.
Text searching
2.
Extremely powerful chemistry searching capabilities:
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Differentiates between reactants and products
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Supports chirality
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Supports rich atom and bond type definitions.
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Mixed field searches supported
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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
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Managing Experimental Protocols
Experiments can be tightly associated with their
protocol, thanks to the notion of a “page”
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A page can have lots of sections, one which contains a
protocol
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Beyond pure text, protocols may be associated
with an E-Notebook in several ways:
1.
2.
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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
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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E-Notebook Supports Direct Data
Acquisition
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Forms can be created to capture of data from any type of
experiment.
Populating forms can be achieved by…
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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:
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Real and integer numbers
Text
Tables
Molecular structures
Images
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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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
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Type checking
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no reaction yields >100%...
can only select “μg”, not “mg”
Field checking: requiring all fields to be filled
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Intellectual Property Protection
E-Notebook provides extremely robust auditing
capabilities:
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When a page is created/saved/printed/changed, a
record of that action is kept in the database.
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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.
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Reporting Capabilities
E-Notebook provides excellent ability to
understand one’s research globally, e.g.:
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Number of experiments involved a given gene
Kinds of experiments were performed on a given
gene
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What hosts were used to produce a vector
What mouse strains where selected as transgene
recipients
Queries can be saved for future use
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… and in fact shared with others…
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Further Important
Considerations
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Knowledge Management Center
http://lane.stanford.edu
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The Importance of (Proper) Backups
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Computers fail…
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1% chance of having hard disk failure in first year of operation…
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HD failure = loosing/damaging physical lab notebook
→ Advantage: backing-up is easy and cheap
Backing up to an external hard disk is good…
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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:
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Exporting to MS Word or Adobe PDF
2.
Exporting database in XML format
3.
Exporting database using E-Notebook’s Administrator tool
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
22
More Questions You Might Have
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Backward compatibility of newer versions of
e-Notebook?
→ CambridgeSoft specifically tests to ensure full
compatible with prior versions of e-Notebook
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→ if you upgrade, you’ll be able to import into current
version
What if you leave Stanford?
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You or your institution can provide a key to your
existing software, which will become unusable
within a year.
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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Questions?
Lane Medical Library &
Knowledge Management Center
http://lane.stanford.edu
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