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 IsotopesCreated by T.B. Coplen, USGS RestonBenjamin Harlow, Stable Isotope Core Facility at Washington State UniversityManaging 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 goLIMS by the USGS is the most readily available, supported, and FREE software for Light Stable IsotopesIf 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 dataHourly drift corrections from multiple standardsLinearity correctionData revision and safeguardsPowerful search, average and export functionsReport and Invoice generationSo 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 LimitationsCan only have as many mass spectrometers or lasers as letters in the English alphabetNormalization by linear regression is all that is currently possibleSome data manipulations may still be required via spreadsheet, etc. prior to importingQuadratic, 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 onlyRequired Security settingsAdd LIMS backend database to “trusted locations”Enable all macros
9 Setup 3 folders, 4 files: Back up Backend DB often! Backend DB (LM8DATA.mdb)Frontend DB (LIMS9 for office 2010.mdb) + Preferences fileBackupBack up Backend DB often!Back up Preference files periodically (especially for new Front end versions)Different users can have their own front end and preferencesCan install on one computer, network, cloudWSU: dropbox; share DB with 7 computers (2 RAID), multiple smartphonesData 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 numberExample: References <1000, samples >1000Keeps 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 neededMore information is better; i.e. project title and account are good to reference laterDo 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 membersMore information is goodBe unique, but avoid special characters
17 Sample excel submission form Customize to your lab: Letterhead, graphics, captionsCaptions must match exactly to what you defined in “special features”Use different forms for different types of samplesProtect certain cells to reduce customer “tinkering”
18 Other features Track lab extraction procedures Make notes about sample prepCreated primarily for offline proceduresCreate labels for samplesUse templates to create run sequences of samples and referencesLable feature is useful for marking your own running standards.
19 Selling (to) yourselfCreate a “client” entry for your lab tests and reference materialWe use “reference” and “test”All international, commercial, and lab developed reference material is logged hereReference lab ID’s get defined in reference table: Automatically fit in a normalizationTest lab ID: treat as a blind sample (Quality Control)
20 IRMS/software setupMachine must use sequential analysis number, with single letter prefix (ex: A-number)Isodat: Configurator > Options > Global settingsEnter old analyses or those without prefix: “concatenate” function in excelNote 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 timeTailor 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
25 Running samplesLIMS ID# “Our lab ID” is most important identifier to use in sample sequencesUse LIMS template or design your own in excelTemplate: 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’sCopy/Paste sample information into a blank tab of the submission worksheetInsert rows for running standards and QC’sCan 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.
29 Exporting results and importing to LIMS Must export specific column headings required by LIMSLine #, Analysis #, time code, gasconfig, area, peak#, identifier 1, delta columns, is ref, comment, RtAll peaks for reference gas must be marked “Is Ref = 1” or removedPerform data preprocessing before importing (i.e. your own linearity, drift or mass fraction corrections)
30 Export tipsIsodat: If a project got created with some special character, don’t export that columnCheck chromatographs prior to exporting. Is reprocessing necessary?Garbage in garbage out
31 Importing dataOption to apply linearity correction at this point
40 Store final results Stores a single value from all accepted reps Marks samples as completedProvides an extra layer of protection to dataNecessary to use LIMS report function
41 Add stored results to in process Unlocks samples for editingCan be done at any timeStore 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 editingThe high and low comment provide two additional storage pointsInclude 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.
44 Can I use LIMS for GCC-IRMS? Yes you can!Treat each vial as a project and target compounds are samples in the projectUse 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 importSort by component (Rt) and time codeAssign the same analysis numberCreate 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 tablesMake your own queries
48 Lab specific queries Annual reports, audits and cost evaluations # days runtime/machine/peripheral/Fiscal year# samples/machine/peripheral/yearCount of customers by country, state, institution, and break down by sample type# of samples billed by typeAverage turnaround by sample typeLong term QC/QA
49 Lab specific queries Annual reports, audits and cost evaluations # days runtime/machine/peripheral/Fiscal year# samples/machine/peripheral/yearCount of customers by country, state, institution, and break down by sample type# of samples billed by typeAverage turnaround by sample typeLong term QC/QA