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Research software for biotechnology laboratories

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.

     

Prepare and track laboratory samples

   
   

How researchers in the field can ask for biotech analysis?

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.      

How to track material along the laboratory protocols?

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

May RnDExp help me avoid sample errors?

Many features in RnDExp that will remove error hazards:

  • Material tracking along the laboratory protocols (scoring, observations, genetic/phenotypic description…)
  • Optimization of listings and forms to reduce the number of manual operations on the samples. 
  • Material identification, enabling “blind” work
  • Barcode handling for inventory and identification of samples, including printer connection and direct identification from the barcode reader

How to share same identification of samples between lab and field?

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.

   

Sample Flow and analysis in Laboratories

   

Can I manage blind analysis?

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.  

Can I track the processing steps required to prepare a sample to analyze?

All the laboratory steps can be set up, followed and monitored:

  • The original material from where is processed a sample is already identified within RnDExp (planted into a RnDExp Experiment and/or inventoried into a RnDExp Stock).
  • The user can build Protocols where will be configured all the processing steps (organized into stages > Operations > Tasks) required to generate a sample which will be the analyzed.
  • User forms, actions traceability and User Access rights (per work stations for example) allow then to have an efficient workflow management for the generation of samples.
  • All transfer of information can be tracked

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)

How to connect an automaton which generates results with sample list?

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

What type of Biotechnology processes can be tracked?

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:

  • To save time in breeding such as Haplo-diploidization, Transgenesis, marker assisted selection, tissue culture;
  • To exploit and characterize genetic diversity such as Population sequencing

RnDExp integrates planning, processing and reporting tools that support daily work of laboratory staff.

     

Managing genomic data and analytics

   

How to manage high-throughput genotyping generating voluminous data?

RnDExp includes some structures optimized for high performances with voluminous data stored. The software optimization includes:

  • Interfaces (possible to automate data centralizing through robots) to store the rough data;
  • Storing facilities to be able to open and view data in an acceptable time and format;
  • Data visualization and data analysis tools which can be used to make decisions.

Can I implement marker assisted breeding program?

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.  

Can I get quick information on big data?

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.

How to improve our trait introgression processes?

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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The expertise of Doriane brings the three players of R&D the resources to organize, share and valorize their research projects:
RESEARCH DEPARTMENTS: Fast implementation of business processes ; Liberation of researchers creativity
IT DEPARTMENTS: Real-time centralization of multilocation data ; Security and integrity of data
MANAGEMENT: Maximization of research investments ; Research departments monitoring ; Intellectual assets valorization and sustainability

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