M2DS: Marker Management Database System

This application is a tool for managing the polymorphic data of markers in F2 or RILs population.

ATTENTION: This Application is still the version of the development environment. Please use on local server. Regarding the use of this application, note that I am not responsible for any loss, damages and troubles.

REQUIREMENTS

Software

• Docker
  • Mac: Docker for Mac
  • Windows: Docker Toolbox

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Getting M2DS

1. Download and Install the Docker software.

   Download site:
   https://www.docker.com/community-edition#/download

2. Start Docker

   If you use MacOS machine, start Terminal.
   See details: https://store.docker.com/editions/community/docker-ce-desktop-mac.

   If you use Windows machine, click the Docker QuickStart icon on your desktop, and start Terminal.
   See details: https://docs.docker.com/toolbox/toolbox_install_windows/#step-3-verify-your-installation

3. Type command on Terminal (using Git):
   git clone https://github.com/qqep685d/M2DS.git
   and
   Move to the directory, M2DS: cd M2DS

4. Type command:
   sh 01_build_app.sh

5. Type command:
   sh 02_create_db.sh

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Basic Usage

Start Terminal on M2DS/.

1. Type command:
   sh 03_run_server.sh

2. Go to the URL on web browser:
   127.0.0.1:8000

3. Use application "M2DS"

   1. Click Add Population
      Input each fields and click OK.
      ("Name" and "Year" are required fields.)

   2. Upload file and Import dataset into database in M2DS.
      M2DS/samples/sample_dataset.txt is an example file.

   3. View records: Strains, Markers and MS Table.

   4. Edit / Delete records.

   5. Download dataset.

4. (Option) You want make M2DS back to the initial state, type command sh 04_clear_app.sh.
   Attention: This command remove some files from M2DS: database file (db.sqlite3), uploaded and download files.

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Dataset File

See the example files:
M2DS/samples/sample_dataset.txt or M2DS/samples/sample_dataset_add.txt

• The first row is header line.

  • The first column is "MARKER". (Don't change!)
  • The second column is "TYPE". (Don't change!)
  • The third column and later are "strain names". You can input arbitrary names.

• The second row and later are each values.

  • The first column is "marker name". You can input arbitrary names. But the duplicated names is not allowed.
  • The second column is "type of marker". Input g or p.
    • g: Genotype (Genetic marker)
    • p: Phenotype (Trait)
  • The third column and later are "marker values of each strain" for the marker. Input A, B, H or -.
    • Genotype
      • A: Homozygous genotype of Parent 1 allele
      • B: Homozygous genotype of Parent 2 allele
      • H: Heterozygous genotype
      • -: missing genotype
    • Phenotype
      • Strings, Integer or Float etc.
      • -: missing value

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Softwares and Python packages included in M2DS

Softwares

• Python (3.6.3)
• SQLite3 (3.19.3)

Python Packages

• Django (2.1.5)
• django-bootstrap4 (0.0.6)
• django-pandas (0.5.1)
• numpy (1.14.2)
• pandas (0.22.0)

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License

This software is released under the MIT License, see LICENSE.