gabywald / biosilico Goto Github PK

Some ideas about Artificial Life, Creatures (game series) and Neural Networks. (Java, Latex, Perl...)

License: GNU General Public License v3.0

Java 61.76% HTML 1.94% Perl 8.77% Makefile 0.17% TeX 26.85% Rich Text Format 0.09% Shell 0.05% Python 0.36%

creatures creatures2 creatures3 norn albia artificial-life artificial-life-algorithms neural-networks neural-networks-from-scratch genetic-algorithm

biosilico's People

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biosilico's Issues

Review Chemicals and Use and Indexes

AntHill Exemple Implementation Part 3

reproduction ReproductionAnima

BioSilico/biosilico-biosilico/src/main/java/gabywald/biosilico/model/reproduction/ReproductionAnima.java

Lines 29 to 33 in bf3b230

 // TODO reproduction ReproductionAnima 

 } 

 }

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

Documentation to be completed with last devs (anthill and reviews)

record neural networks / lobes !

BioSilico/biosilico-biosilico/src/main/java/gabywald/biosilico/model/Organism.java

Lines 565 to 568 in bf3b230

 // ***** TODO record neural networks / lobes !  

 } else { result.append("NO DATA ABOUT BRAIN, LOBES AND NEURONS\n"); } 

 return result.toString();

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

Add uses of data pipelines in bioinformatics

Snakemake
Nextflow
Galaxy
Knime
Pipeline Pilot ?

AntHill Exemple Implementation

Some ressources to add (links and articles)

AntHill Exemple Implementation Part 5

More Tests Decision Part 2

// TODO Decision DEATH
// TODO Decision REST
// TODO Decision SLEEP
// TODO Decision EMIT
// TODO Decision RECEIVE
// TODO Decision HAS
// TODO Decision IS
// TODO Decision LAY_EGG
// TODO Decision MATE

reproduction ReproductionBacta

BioSilico/biosilico-biosilico/src/main/java/gabywald/biosilico/model/reproduction/ReproductionBacta.java

Lines 28 to 32 in bf3b230

 // TODO reproduction ReproductionBacta 

 } 

 }

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

More review

TODO Java 8 streams
TODO more Unit Tests
TODO retake some units tests

Externalize / Templatize Decision

IDecision + DecisionBuilder + specific code package

Auto-generated catch block

BioSilico/biosilico-crypto/src/test/java/gabywald/crypto/data/ioput/tests/GenBankFileReaderTests.java

Lines 32 to 37 in bf3b230

 // TODO Auto-generated catch block 

 e.printStackTrace(); 

 } 

 Assertions.assertNotNull( content01 ); 

 String[] content2read = content01.split("\\*\\*\\*\\*\\* \\*\\*\\*\\*\\* \\*\\*\\*\\*\\* \\*\\*\\*\\*\\* \\*\\*\\*\\*\\* \n");

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

Make World / WorldCase generic (IEnvironment + IEnvironmentItem + Builders)

Permit Other Implementations !

GraphicalEditing View for Genome + Organism

Reuse what is existing and make it in one application

Gene Creator (types of genes, pathway...)
Genetic Kit (create an Organism, select GeneS, PathwayS...)
Organism Kit

=> module biosilico-biosilico ;

gabywald.biosilico.launchers
gabywald.biosilico.view

Some ideas :

different tabs for each specific view
interactive selection of an organism
direct view of "Chemical Variables" and modifications (a matrix and a selector)
direct view of "Brain Network" (a matrix)
interactive view of states of an Organism
...

Add some Enums

Agent types
Status types
Directions in World

Add Gene Builder (Design Pattern)

Reproduction ReproductionViria

BioSilico/biosilico-biosilico/src/main/java/gabywald/biosilico/model/reproduction/ReproductionViria.java

Lines 28 to 32 in bf3b230

 // TODO reproduction ReproductionViria 

 } 

 }

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

More Tests Organism

gabywald.biosilico.model.tests.OrganismInWorldCaseTests

Review and modify old parts

Structures : Listes / Lists and others...
Make modules
Externalize parts which need it
Remake tests
Remake some tutorials
...

to change it / values !! (Gamet and fertilty)

BioSilico/biosilico-biosilico/src/main/java/gabywald/biosilico/model/Organism.java

Lines 423 to 428 in bf3b230

 // ***** Increase Gamet TODO to change it / values !! 

 this.variables.setVarPlus(920, 50); 

 } 

 } 

 private void decisionToLayEgg() { /** XXX */

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

Add Unit Tests

Permit review of neural network classes and constructions
Permit better review of genetic related classes

More Tests Decision

gabywald.biosilico.model.decisions.tests.DecisionsTests

Create title for generated references

... */

BioSilico/biosilico-crypto/src/main/java/gabywald/crypto/data/ioput/BiologicalFileCreatorHelper.java

Lines 125 to 130 in bf3b230

 /** TODO ... */ 

 toReturn = "title of the reference"; 

 return toReturn; 

 }

This comment was generated by todo based on a `TODO` comment in `bf3b230` in #23. cc @gabywald.

Originally posted by @todo in #23 (comment)

Review and reorganise code

Include also adding older source code !

Maven modules to part source code ;
Rejuvenate source code (newer version of java : generic types and lambda expressions)

More Tests Reproduction

gabywald.biosilico.model.reproduction.tests.ReproductionTests

Reproduction Viridita / Plants

Generators of genetic data files (Embl, GenBank, FASTA)

Permit other implementations of Chemicals

Interface IChemicals, ChemicalsBuilder...
Now is a list of a thousand elements (noll all attributed) ; idea is to permit another implementation (i.e. for example a Mendeliev classication modelisation, complex molecules, find by name...)

	// ***** TODO record neural networks / lobes !
	} else { result.append("NO DATA ABOUT BRAIN, LOBES AND NEURONS\n"); }

	return result.toString();

	// TODO Auto-generated catch block
	e.printStackTrace();
	}
	Assertions.assertNotNull( content01 );
	String[] content2read = content01.split("\\\\\\\\\\* \\\\\\\\\\* \\\\\\\\\\* \\\\\\\\\\* \\\\\\\\\\* \n");

	// ***** Increase Gamet TODO to change it / values !!
	this.variables.setVarPlus(920, 50);
	}
	}

	private void decisionToLayEgg() { /** XXX */

	/** TODO ... */
	toReturn = "title of the reference";

	return toReturn;
	}

gabywald / biosilico Goto Github PK

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biosilico's Issues

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

This issue was generated by todo based on a TODO comment in bf3b230 when #23 was merged. cc @gabywald.

... */

This comment was generated by todo based on a TODO comment in bf3b230 in #23. cc @gabywald.

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This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This issue was generated by todo based on a `TODO` comment in `bf3b230` when #23 was merged. cc @gabywald.

This comment was generated by todo based on a `TODO` comment in `bf3b230` in #23. cc @gabywald.