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From samples to results: How Biotech labs support decision making in field experiments
Biotechnology laboratories take in charge the analysis or transformation of samples collected from living material. The data or products generated are vital for the breeders or testers for decision making and/or breeding progress. Faster and accurate lab results enable them to take better decisions sooner.
Laboratories use many different types of automata for faster and more consistent analyses, generating important amounts of data in various computer files formats. One of the challenges they face, which has nothing to do with their core business is: feeding sample lists to automata and generating result files linked to each sample in a standardized format. That is why it is crucial to build the bridges when possible and to translate to standard formats when not.
Another key point is the communication with researchers. Lists of material and conditions must be adapted to sample collection and processing. Then it is important to make sure the generated data or sample is accessible in the researcher’s work environment.
Biotechnology laboratories independent or not, need to be very thorough and reactive to the evolutions of new technologies. Standardization and upgradability of RnDExp ensures consistency of processes and adaptiveness to new technologies.
Furthermore, RnDExp is a centralized system that manages lists of elements, being samples, tests or results and offers many customizable outputs: printout reports, spreadsheets, labels. Therefore, RnDExp helps biotechnology laboratories better communicate with their researcher clients.
Field researchers and laboratory working on the same centralized database system are sharing same material reference and IDs.
Separate working station can be configured within RnDExp to enable two distinctive areas to share some information but to visualize/capture distinctive data. It is how are managed queries for analysis to a further department with separated working stations on the same material references.
RnDExp proposes each organization to define
1) the type of samples manipulated e.g. vegetative parts of the plants, DNA extracted, transformed material, with all their characteristics
2) the source from where it has been collected (e.g. identifier of the plant in a field plot, the person who send or prepared the sample)
3) the processing steps it must walk through.
RnDExp is process oriented thanks to flexible tools to select and display distinct information
Many features in RnDExp that will remove error hazards:
Good organization of material identification and recognition is crucial to share real material in a multi area working system. Using labels to identify the source material can be very useful. The process of recognition can be even more optimized with the use of bar codes (managed by RnDExp) particularly to make an inventory of the list of samples shipped to be processed.
Material identification and labels management ensuring the integrity of data and facilitating the work flow are one of the key features included in RnDExp projects.
RnDExp can manage multi identification depending on user profiles. Particularly generating generic sample ID which does not translate directly the nature/origin of the sample is possible through specific interfaces. They are only accessible for users in charge of entering results and who do not have the right to know the nature of the sample to ensure the objectivity of results.
All the laboratory steps can be set up, followed and monitored:
Particularly for genomic sequencing, a stock of reagents and containers can be inventoried, managed and tracked for the preparation of DNA sequences to be analyzed (e.g. PCR steps)
RnDExp database is open to any external system/database that generates data with same identification keys on samples. On demand, one RnDExp specific interface tool enable to capture and store automatically data from a sequencer connected through serial port. It saves time (in data transfers and importation) and guarantees security of data (without manual manipulation).
The same possibilities are available offline within RnDExp Mobile application
Process description is the 1st step towards work optimization through digitalization and automation.
Any biotech process implying living material walking through successive steps can be implemented within RnDExp thanks to highly configurable protocols. For example:
RnDExp integrates planning, processing and reporting tools that support daily work of laboratory staff.
RnDExp includes some structures optimized for high performances with voluminous data stored. The software optimization includes:
A list of targeted genes within a breeding program can be implemented in RnDExp once they are correlated with the loci and sequence and/or the marker.
Storing of marker descriptions (genomic sequences, marking techniques, alleles) in RnDExp and using the tailored data visualization tools help breeders select lines which incorporated the targeted gene.
Marking results combined with these visualization tools can notably help breeders find in the fields which inbred line to promote, which backcross still has the targeted trait to continue the introgression.
RnDExp powerful architecture enables high performances for huge volumes of data stored (within 1 min. displays 100,000 X 1,000 data matrix).
Several algorithms are under disposal of the scientists like dendrograms and genetic distance calculations to study a population.
Advanced views can combine Genetic results with Phenotype observations to help breeders in making decisions.
Several methods for traits introgression can be managed within RnDExp, through Backcross (cf. Breeding activity) or through Biotechnology methods detailed above.
RnDExp centralizes trait introgression process management with field evaluation which make easier the tracking of material that implemented the targeted trait without impacting agronomical responses.
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