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Our in-house Django-based tool to register genetic samples and make automatic conclusions for genetic reports. Currently only admin interface is used.

Installation

  • clone the repository: git clone [email protected]:babinyurii/lab_genetic_reporter.git
  • run migrations: python manage.py makemigrations, python manage.py migrate
  • run tests: python manage.py test
  • run the project: python manage.py runserver or adapt the run.bat file for your project location

Workflow

Preparation of SNP, detection kits and conlusion templates

1. create database of SNPs

  • go to Markers app, SNPs section
  • create SNPs which are used in your detection kits

2. create database of detection kits

  • go to DETECTION_KITS, SNP detection kits section
  • create detection kits and link SNPs which are used in your kits

3. create report rules

Report rule links any two SNPs together (which is the simplest haplotype) in any kit. Report rule consists of 9 genotype combinations which have clinical significance for final report

  • go to SNP SAMPLES AND RESULTS app, 1. Report rules for two SNP section
  • create report rule: choose two SNPs and link the rule to one or more detection kits

When report rule is created, its 9 genotype combinations are generated in the section 2. report rules: conclusions for genotype combinations

4. fill in the conclusion text associated with each genotype combination

  • go to SNP SAMPLES AND RESULTS, section 2. report rules: conclusions for genotype combinations
  • click each of the report rule and fill in the report section

Working with samples

1. add sample

  • go to SNP SAMPLES AND RESULTS, section 3. Samples
  • add sample and choose the detection kit which is used for research

When sample is saved, the template for its results is generated in the section 4. SNP results

2. fill in the results after research

  • go to SNP SAMPLES AND RESULTS, section 4. SNP results
  • fill in the genotype results for each result record

When the last result for a particular sample is saved, the conlusion based on the report rule genotype combinations is generated in the SNP SAMPLES AND RESULTS, section 5. Conclusions for reports