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Is there life after LIMS?

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Presentation on theme: "Is there life after LIMS?"— Presentation transcript:

1 Is there life after LIMS?
No, but thankfully there is beer. LIMS for Light Stable Isotopes Created by T.B. Coplen, USGS Reston Benjamin Harlow, Stable Isotope Core Facility at Washington State University Managing machines is an important component. Managing all the data generated is perhaps a bigger component and can span the lifetime of numerous machines. I remember ing Ty Coplen about 5 pm PST back in that I was thinking about trying LIMS. About 30s later I got a phone call from Ty saying “Yes you should”. I missed opportunities for any formal training so I set it up myself. In about a week I was using LIMS exclusively and have never looked back. Due to my frequent pestering and suggestions, our lab has been a beta test site for new versions since Basically he asks us to try to break it and so far he keeps fixing it.

2 Is LIMS for you? Do you process >100 samples per year?
Do you process samples for multiple clients? Do you measure multiple isotopes? Do you use more than one instrument? Our data processing and storage snowballs as we add samples, clients and services. Keeping track of it all and keeping errors to a minimum can be a real challenge.

3 Is LIMS for you… Do you already have a database or spreadsheets that work for you? LIMS by the USGS is not the only way to go LIMS by the USGS is the most readily available, supported, and FREE software for Light Stable Isotopes If yes, start sooner rather than later! Building a database is like growing an onion. Layers and layers build with time. You want all those layers in your database. I analyzed samples for about 1y before using LIMS

4 Thankfully there is beer.
This is how much I owe Ty Coplen

5 Benefits to using LIMS All your information in one place
Rapid and consistent treatment of data Hourly drift corrections from multiple standards Linearity correction Data revision and safeguards Powerful search, average and export functions Report and Invoice generation So many details are readily available, which makes our job easier. For example, one can track normalizations for a specific isotope from a specific machine. One can also export samples ran during specific time periods or on a specific machine. Or one can recall all references interspersed with a range of samples.

6 Limitations Can only have as many mass spectrometers or lasers as letters in the English alphabet Normalization by linear regression is all that is currently possible Some data manipulations may still be required via spreadsheet, etc. prior to importing Quadratic, logarithmic, curvilinear data correction is not currently an option. Some users also may prefer to use their own drift and linearity corrections outside of LIMS. Elemental calculations may also be preferred outside of LIMS. Being able to correct outside of LIMS may add time but can also be useful.

7 First things first MS Access supported versions
MS Office 2007, 2010, 32 bit only Required Security settings Add LIMS backend database to “trusted locations” Enable all macros

8 Set trusted locations, macros

9 Setup 3 folders, 4 files: Back up Backend DB often!
Backend DB (LM8DATA.mdb) Frontend DB (LIMS9 for office 2010.mdb) + Preferences file Backup Back up Backend DB often! Back up Preference files periodically (especially for new Front end versions) Different users can have their own front end and preferences Can install on one computer, network, cloud WSU: dropbox; share DB with 7 computers (2 RAID), multiple smartphones Data sharing options make data access and backups easier. LIMS automatically creates backups every time it closes. So backups are created on multiple computers if it is shared. The cloud works well for us, but is not without potential pitfalls. LIMS does have locking functions to protect edits in progress, but it may not be foolproof. If working on the database and you loose network connectivity, updates may be delayed and create conflicted versions. We still try to avoid overlap if doing any type of editing function. A new database viewer is available for read only access.



12 Import project to LIMS Manual entry or Excel spreadsheet
Concept of “placeholders” Adjusting the next “Our Lab ID” Reference ID’s often set as a low number Example: References <1000, samples >1000 Keeps all references in one area of the sample table


14 Enter new clients manually before creating the first project for that client

15 Adding a project manually
Date, Name, Media is the minimum information needed More information is better; i.e. project title and account are good to reference later Do not enter duplicate ID’s and avoid special characters for sample IDs

16 Submit to LIMS Simple excel templates are available for modification
Reduces typographical errors and valuable time of lab members More information is good Be unique, but avoid special characters

17 Sample excel submission form
Customize to your lab: Letterhead, graphics, captions Captions must match exactly to what you defined in “special features” Use different forms for different types of samples Protect certain cells to reduce customer “tinkering”

18 Other features Track lab extraction procedures
Make notes about sample prep Created primarily for offline procedures Create labels for samples Use templates to create run sequences of samples and references Lable feature is useful for marking your own running standards.

19 Selling (to) yourself Create a “client” entry for your lab tests and reference material We use “reference” and “test” All international, commercial, and lab developed reference material is logged here Reference lab ID’s get defined in reference table: Automatically fit in a normalization Test lab ID: treat as a blind sample (Quality Control)

20 IRMS/software setup Machine must use sequential analysis number, with single letter prefix (ex: A-number) Isodat: Configurator > Options > Global settings Enter old analyses or those without prefix: “concatenate” function in excel Note analysis number if you ever restore IRMS software! If you ever had to restore a computer or in the case of Isodat use version handler, you may note the analysis number resets to an earlier time. Noting the analysis number range is also a very useful way to separate analyses from a specific day, time period or machine.

21 Know your media KISS IT More classifications can be useful
Can add more at any time Tailor specific to your lab

22 Media Media originally designed for 2 isotopes only!
It is possible to store, edit and average 4. How? Stay tuned

23 Procedure Codes

24 Low and High procedure Codes

25 Running samples LIMS ID# “Our lab ID” is most important identifier to use in sample sequences Use LIMS template or design your own in excel Template: LIMS automatically designs sample sequence

26 Other features: Creating a sample list/template

27 Another way to make a run sequence
Import excel file and generate LIMS ID’s Copy/Paste sample information into a blank tab of the submission worksheet Insert rows for running standards and QC’s Can customize to instrument service state, sample types, desired timing, etc. Example: sometimes we run for one element only which requires different standards. We like to run plant standards/weights with plant samples vs protein with protein. Also some samples like filters or hard to combust samples may repeat standards more frequently. Maximize throughput: calculate runtime of partial sequence to finish in time to start evening sequence.

28 Then you run the samples
What Paul said…

29 Exporting results and importing to LIMS
Must export specific column headings required by LIMS Line #, Analysis #, time code, gasconfig, area, peak#, identifier 1, delta columns, is ref, comment, Rt All peaks for reference gas must be marked “Is Ref = 1” or removed Perform data preprocessing before importing (i.e. your own linearity, drift or mass fraction corrections)

30 Export tips Isodat: If a project got created with some special character, don’t export that column Check chromatographs prior to exporting. Is reprocessing necessary? Garbage in garbage out

31 Importing data Option to apply linearity correction at this point


33 3 point normalization example

34 Add elemental and blank corrections

35 Normalize std gasses and data
Seldom used Must import and properly code ref gasses Provides option to salvage data

36 Applying an hourly drift correction
Use drift from any single standard Override: combination of all accepted standards, or custom Apply two drifts: must break up the sequence into two corrections

37 Evaluating/editing samples in progress
Mean, SD and outlier information Note: When samples are “in progress” mean, SD are available Some may choose to report at this point

38 Rapid tracking of QC/QA

39 Export full results for samples

40 Store final results Stores a single value from all accepted reps
Marks samples as completed Provides an extra layer of protection to data Necessary to use LIMS report function

41 Add stored results to in process
Unlocks samples for editing Can be done at any time Store function may be unnecesary for some users

42 Storing an additional isotope or other numeric data
The “comment” field now averages numeric values and allows editing The high and low comment provide two additional storage points Include data calculated by a different detector, i.e. CNHOS% Use with procedures that generate data for more than two isotopes, i.e. thermal conversion of N2O.

43 Invoice generation and payment tracking

44 Can I use LIMS for GCC-IRMS?
Yes you can! Treat each vial as a project and target compounds are samples in the project Use Rt or component ID feature in LIMS (extraction ID, Comment, Rt) Internal standards should be in each vial

45 Can I use LIMS for GCC-IRMS?
Alternative method: Modify file to import Sort by component (Rt) and time code Assign the same analysis number Create unique peak number for every compound in a sample

46 Can I use LIMS for Lasers?
Yes you can! See Len Wassenaar’s session on Wednesday

47 More Advanced Open the tables and look in there
Cut, copy, paste; but watch for linked tables Make your own queries

48 Lab specific queries Annual reports, audits and cost evaluations
# days runtime/machine/peripheral/Fiscal year # samples/machine/peripheral/year Count of customers by country, state, institution, and break down by sample type # of samples billed by type Average turnaround by sample type Long term QC/QA

49 Lab specific queries Annual reports, audits and cost evaluations
# days runtime/machine/peripheral/Fiscal year # samples/machine/peripheral/year Count of customers by country, state, institution, and break down by sample type # of samples billed by type Average turnaround by sample type Long term QC/QA

50 Questions?

51 What if… I need to delete a project I entered the wrong media code
I can’t find my samples in LIMS


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