Merge pull request #1 from dyaus-dev/develop

Update files

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at himoto@protein.osaka-u.ac.jp. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

.github/workflows/build.yml

@@ -0,0 +1,32 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install biomass tqdm pytest
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -7,6 +7,11 @@ figure/
 
 # fit_param
 out/
+!/training/erbb_network_jl/dat2npy/out/
+
+# patient-specific models
+TCGA_*
+!/models/breast/TCGA_3C_AALK_01A
 
 # sensitivity array
 sensitivity_coefficients/
@@ -21,7 +26,7 @@ optimization_results/
 errout/
 
 # transcriptomic data
-transcriptomic_data/
+transcriptomic_data/*.csv
 
 # Python ---
 
@@ -82,22 +87,6 @@ cover/
 *.mo
 *.pot
 
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 .pybuilder/
 target/
@@ -142,12 +131,12 @@ vignettes/*.pdf
 .httr-oauth
 
 # knitr and R markdown default cache directories
- *_cache/
- /cache/
+*_cache/
+/cache/
 
 # Temporary files created by R markdown
- *.utf8.md
- *.knit.md
+*.utf8.md
+*.knit.md
 
 # R Environment Variables
 .Renviron

README.md

@@ -1,6 +1,7 @@
-# dyaus_breast
+# breast_cancer
 
-[![License](https://img.shields.io/badge/License-Apache%202.0-brightgreen.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Actions Status](https://github.com/dyaus-dev/breast_cancer/workflows/Tests/badge.svg)](https://github.com/dyaus-dev/breast_cancer/actions)
+[![License](https://img.shields.io/badge/License-Apache%202.0-green.svg)](https://github.com/dyaus-dev/breast_cancer/blob/master/LICENSE)
 
 Workflow for classifying breast cancer subtypes based on intracellular signaling dynamics.
 
@@ -12,13 +13,7 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
 | Julia >= 1.5  | [BioMASS.jl](https://github.com/himoto/BioMASS.jl)                                             |
 | R             | [TODO] Write dependent packages here.                                                          |
 
-## Individualization of the mechanistic model
-
-### Integrate TCGA and CCLE data
-
-[TODO] Write analysis procedure here.
-
-### Build an executable model of the ErbB signaling network
+## An executable model of the ErbB network dynamics
 
 1. Use `biomass.Text2Model` to build a mechanistic model
 
@@ -28,10 +23,12 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
    Text2Model("models/erbb_network.txt").to_biomass()
    ```
 
-1. Rename **erbb_network/** to CCLE_name or TCGA_ID
+1. Rename **erbb_network/** to CCLE_name or TCGA_ID, e.g., **MCF7_BREAST** or **TCGA_3C_AALK_01A**
 
 1. Edit **name2idx/parameters.py**
-   - Add weighting factors (`'w_XXX'`)
+
+   - Add weighting factors for each gene (prefix: `"w_"`)
+
 1. Edit **set_search_param.py**
 
    - Import `dyaus.Individualization`
@@ -86,22 +83,30 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
        for i, j in enumerate(self.idx_initials):
            y0[j] = indiv[i + len(self.idx_params)]
 
-       x[C.V291] = incorporating_gene_expression_levels.as_maximal_transcription_rate(
+       # As maximal transcription rate
+       x[C.V291] = incorporating_gene_expression_levels.as_reaction_rate(
            __path__[0].split(os.sep)[-1], x, "V291", "DUSP"
        )
-       x[C.V310] = incorporating_gene_expression_levels.as_maximal_transcription_rate(
+       x[C.V310] = incorporating_gene_expression_levels.as_reaction_rate(
            __path__[0].split(os.sep)[-1], x, "V310", "cMyc"
        )
-       y0 = incorporating_gene_expression_levels.as_initial_condition(
+       # As initial conditions
+       y0 = incorporating_gene_expression_levels.as_initial_conditions(
            __path__[0].split(os.sep)[-1], x, y0
        )
 
        ...
    ```
 
-### Train model parameters against time-course datasets obtained from breast cancer cell lines
+## Individualization of the mechanistic model
+
+### Integrate TCGA and CCLE data
+
+[TODO] Write analysis procedure here.
+
+### Use time-course datasets to train kinetic constants and weighting factors
 
-1. Use `biomass.Text2Model` to build a mechanistic model for parameter estimation with BioMASS.jl
+1. Build a mechanistic model for parameter estimation with BioMASS.jl
 
    ```python
    from biomass import Text2Model
@@ -120,17 +125,38 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
    $ cd training
    $ mkdir errout
    $ sh optimize_parallel.sh
+   $ cd ..
    ```
 
    When finished, run:
 
    ```julia
    using BioMASS
 
-   param2biomass(".")
+   param2biomass("training")
    ```
 
-   And you will get **dat2npy/out/**. This is the optimized parameter sets that biomass can load. Copy **out/** to each biomass model folder.
+   And you will get **dat2npy/out/**. This is the optimized parameter sets that biomass can load.
+   Copy **out/** to each biomass model folder via:
+
+   ```python
+   import os
+   import shutil
+
+   models = []
+   path_to_models = os.path.join("models", "breast")
+   for f in os.listdir(path_to_models):
+        if os.path.isdir(os.path.join(path_to_models, f)) and (
+            f.startswith("TCGA_") or f.endswith("_BREAST")
+        ):
+            models.append(f)
+   # Set optimized parameter sets
+   for model in models:
+       shutil.copytree(
+           os.path.join("training", "dat2npy", "out"),
+           os.path.join(path_to_models, f"{model}", "out"),
+       )
+   ```
 
 ### Execute patient-specific models
 
@@ -143,33 +169,17 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
    from dyaus import PatientModelSimulations
 
 
-   with open (
-       os.path.join(
-           "models",
-           "breast",
-           "sample_names.txt",
-       ), mode="r"
-   ) as f:
+   with open (os.path.join("models", "breast", "sample_names.txt"), mode="r") as f:
        TCGA_ID = f.read().splitlines()
-
    # Create patient-specific models
    for patient in TCGA_ID:
        if patient != "TCGA_3C_AALK_01A":
            shutil.copytree(
-               os.path.join(
-                   "models",
-                   "breast",
-                   "TCGA_3C_AALK_01A",
-               ),
-               os.path.join(
-                   "models",
-                   "breast",
-                   f"{patient}",
-               )
+               os.path.join("models", "breast", "TCGA_3C_AALK_01A"),
+               os.path.join("models", "breast", f"{patient}"),
            )
-
+   # Execute patient-specific models
    simulations = PatientModelSimulations("models.breast", TCGA_ID)
-
    simulations.run()
    ```
 
@@ -179,4 +189,4 @@ Workflow for classifying breast cancer subtypes based on intracellular signaling
 
 ## License
 
-[Apache-2.0 License](https://opensource.org/licenses/Apache-2.0)
+[Apache License 2.0](LICENSE)

dyaus_dev/__init__.py

@@ -0,0 +1,10 @@
+"""Dynamics-driven automatic subtyping"""
+
+__author__ = ", ".join(["Hiroaki Imoto", "Sawa Yamashiro"])
+__maintainer__ = "Hiroaki Imoto"
+__email__ = "himoto@protein.osaka-u.ac.jp"
+__version__ = "0.0.1"
+
+
+from .individualization import Individualization
+from .patient_model import PatientModelAnalyses, PatientModelSimulations