Informatics and Biobanking

A presentation on Informatics and Biobanking highlighting novel tools of data collection being used by ilri. In addition it also focuses on the Biobanking and Biopreservation platform at ilri.

Transcript

1. Informatics & BioBanking By: Kihara Absolomon
2.  Introduction  BioBanking  Sample Collection  Data  LIMS  Backup and Security  Custom Modules  Acknowledgements
3. What is a Biobank? Biobanked samples have: Great 'metadata' Visible to potential collaborators (typically via a web interface) Simple tracking (typically barcoding) Very safe storage (typically in LN) Access arrangements
4. Why Biobank? Three overwhelming reasons: Maximise the return on expensive sampling trips – Use the same sample to ask multiple questions now and in the future. Maximise the understanding of the biology – different pieces of information about identical samples. Maximise the value for your study from your sample – the requirements for biobanking force improvements on your sampling methods
5. Why Biobank? Sampling is a very time-consuming and expensive exercise. We have an ethical and scientific responsibility to make the best use of that effort and money.
6.  Introduction  BioBanking  Sample Collection  Data  LIMS  Backup and Security  Custom Modules  Acknowledgements
7. Actual sample collection Sample & Data Collection... Life Cycle Preparation  Label printing  Pre-labelling  Systems preparation Database Update  Backup of temp dbase  Update LIMS(master db) Data Processing  Check data integrity  Logging of samples  Processing GPS Coordinates  …etc
8. …/sample & data collection Wildlife Sampling  Whole Blood  Serum  Tissues Random Livestock Sampling  Whole Blood  Serum Vector Sampling  Mosquitoes  Ticks Sentinel Herd Sampling  Whole Blood  Serum Human Samples Collection  Whole Blood  Serum Chicken Sampling Blood on FTA  Tissues  Filled in questionnaires Goat Sampling  Whole Blood  Serum Buffy Coat
9. tarakibu
10. tarakibu fundamentals • All animals are unique and must have a unique identifying ID or name. • The animal basic metadata is captured when the animal is recruited into a study. This metadata includes unique name, species, sex, DOB, date & time of recruitment, GPS coordinates • Samples are only tied to the 'thing' they come from during sampling. • All samples MUST bear a GPS coordinate of where they were collected from, a timestamp of when they were collected and the person responsible for them. All samples are UNIQUE and MUST be barcoded.
11. ukasimu
12. ukasimu basics • All samples are unique, barcoded and have the corresponding metadata. • Aliquots of samples are unique by themselves and must bear a unique name and must be barcoded. • Aliquots are stored in unique trays and in specific positions. ukasimu extends the notion that all samples are unique and so are their children.
13. ODK Suite Swiss army knife in data collection ­ ODK Validate, Collect, Aggregate, Briefcase ­ Mobile based data collection system ­ Open source, highly extensible • Questionnaire based • GPS • Barcodes • Pictures • Voice • Video
14. ODK Collect
15. ../and now...  Introduction  BioBanking  Sample Collection  Data  LIMS  Backup and Security  Custom Modules  Thanks
16. Samples Types • Sample Types • Bacteriology fecal isolates • Serum decanted from heparinised blood at final visit • Thick blood smears from jugular blood • Bacterial isolates from mastitic milk • Thin blood smears from jugular blood • Plasma for cytokines • Daughter samples from Heparinised blood collected in all clinical episodes • Blood in magic buffer for genetics • Thick blood smears from marginal ear vein blood • Milk samples • Thin blood smears from marginal ear vein blood • New methylene blue slides • EDTA blood collected during routine visits • Plasma in RNALater buffer collected during a final visit
17. …more samples • Serum samples from routine visits • Clinical miscellaneous samples • Whole blood collected in an EDTA vacutainer • Blood for serum • Miscellaneous sample • DNA sample • RNA sample • Serum Sample • Blood stored in an FTA card • Whole Blood • Clocal Swabs • Oral Swabs • Ticks • Tissues
18. ../then..  Introduction  BioBanking  Sample Collection  Data  LIMS LIMS  Backup and Security  Custom Modules  Thanks
19. LIMS
20. …/and more…
21. …/more
22. moving on swiftly...  Introduction  BioBanking  Sample Collection  Data  LIMS  Backup and Security  Custom Modules  Thanks
23. Backup You may call it too much...we call it paranoia... Hourly snapshots of the whole system (external) Daily snapshots of the dbase at 3.15am (internal) Incremental Backups every day (Backuppc) Full Backups every 5 days (Backuppc) Daily dbase snapshots sync'd to the cloud Manual backups when updating the dbase (user or system initiated – internal) Backuppc data saved on a RAID which provides increased storage functions and reliability through redundancy “We've got a good system in place. Guys know their roles, and we've got capable backup. If Mike isn't 100 percent, then Matt will step right in.”
24. Security Physical server in a secure room The server is behind ILRI's firewall Very few people have accounts on the physical server ALL collaborators have access to ALL the data via tools and systems that we have developed If you want total security, go to prison. There you're fed, clothed, given medical care and so on.... - Dwight D. Eisenhower
25. a bit of this a bit of that...  Introduction  BioBanking  Sample Collection  Data  LIMS  Backup and Security  Custom Modules  Thanks
27. AVID Resources  http://azizi.ilri.cgiar.org/ - AVID home page  http://azizi.ilri.cgiar.org/avid/  http://azizi.ilri.cgiar.org/labcollector/ - LIMS  http://azizi.ilri.cgiar.org/avid_drupal7/  http://azizi.ilri.cgiar.org/entomology/  http://azizi.ilri.cgiar.org/photo_gallery/ - AVID photos  http://azizi.ilri.cgiar.org/wx/ - Weather satellite images  ...and more still being developed
28. asante, thanks, merci, spasiba... THANKS • The AVID team (ICIPE, KWS, KARI, DVS, MoPHS, KEMRI, ILRI) •The Genomics Group at ILRI • Kemp Steve • Michuki George • Rumberia Cecilia • Orth Alan • Ogugo Moses •DGEA Project •IDEAL Project …. questions….