diff --git a/cases/0001/index0.heta b/cases/0001/index0.heta index d43834d..e9f1774 100644 --- a/cases/0001/index0.heta +++ b/cases/0001/index0.heta @@ -16,6 +16,3 @@ r1 @Reaction {actors: s1 => } := k1 * s1 * comp1; // constant of reaction k1 @Const = 0.01; - -// export format -#export {format: SBML}; diff --git a/cases/0001/index1.heta b/cases/0001/index1.heta deleted file mode 100644 index bf4050b..0000000 --- a/cases/0001/index1.heta +++ /dev/null @@ -1,21 +0,0 @@ -/* - Simple Heta model exported to SBML, JSON and YAML formats. -*/ -// index.heta - -// compartment of size 1 -comp1 @Compartment .= 1; - -// species with initial concentration 10 -s1 @Species {compartment: comp1} .= 10; - -// reaction of s1 degradation -r1 @Reaction {actors: s1 => } := k1 * s1 * comp1; - -// constant of reaction -k1 @Const = 0.01; - -// export format -#export {format: SBML}; -#export {format: JSON}; -#export {format: YAML}; diff --git a/cases/0001/index4.heta b/cases/0001/index4.heta deleted file mode 100644 index b60062f..0000000 --- a/cases/0001/index4.heta +++ /dev/null @@ -1,30 +0,0 @@ -/* - Create simple Heta model. - Add all available export formats with default file names and default options. -*/ -// index.heta - -// compartment of size 1 -comp1 @Compartment .= 1; - -// species with initial concentration 10 -s1 @Species {compartment: comp1} .= 10; - -// reaction of s1 degradation -r1 @Reaction {actors: s1 => } := k1 * s1 * comp1; - -// constant of reaction -k1 @Const = 0.01; - -// export format -#export {format: JSON}; -#export {format: YAML}; -#export {format: DBSolve}; -#export {format: SBML}; -#export {format: Simbio}; -#export {format: Mrgsolve}; -#export {format: Table}; -#export {format: Julia}; -#export {format: Matlab}; -#export {format: Dot}; -#export {format: Summary}; diff --git a/cases/0001/index5.heta b/cases/0001/index5.heta deleted file mode 100644 index f0fb315..0000000 --- a/cases/0001/index5.heta +++ /dev/null @@ -1,41 +0,0 @@ -/* - Create simple Heta model. - For the same model add as many as possible available export options. -*/ -// index.heta - -// compartment of size 1 -comp1 @Compartment .= 1; - -// species with initial concentration 10 -s1 @Species {compartment: comp1} .= 10; - -// reaction of s1 degradation -r1 @Reaction {actors: s1 => } := k1 * s1 * comp1; - -// constant of reaction -k1 @Const = 0.01; - -// export format -// another directory name, long format of units -#export {format: JSON, filepath: xxx, noUnitsExpr: true}; -// long format of units -#export {format: YAML, noUnitsExpr: true}; -// use pow(x, y) instead of x^y in the output, group constants by the first tag, use old format of SLV file -#export {format: DBSolve, powTransform: function, groupConstBy: "tags[0]", version: 25}; -// use Level 3 version 2 -#export {format: SBML, version: L3V2}; -// another directory name for output directory -#export {format: Simbio, filepath: yyy}; -// another directory name for output directory -#export {format: Mrgsolve, filepath: zzz}; -// omit 3 rows between header and data, use multiple sheets in the output -#export {format: Table, omitRows: 3, bookType: xlsx}; -// another directory name for output directory -#export {format: Julia, filepath: www}; -// another directory name for output directory -#export {format: Matlab, filepath: qqq}; -// another directory name for output directory -#export {format: Dot, filepath: ppp}; -// another directory name for output directory -#export {format: Summary, filepath: ooo}; diff --git a/cases/0002/index0.heta b/cases/0002/index0.heta index e115b4d..e80b208 100644 --- a/cases/0002/index0.heta +++ b/cases/0002/index0.heta @@ -16,6 +16,3 @@ r1 @Reaction {actors: s1 -> p1} := k1 * s1 * comp1; // reaction constant k1 @Const = 0.1; - -// export format -#export {format: SBML}; diff --git a/cases/0002/index1.heta b/cases/0002/index1.heta index 23877b0..31aeaa4 100644 --- a/cases/0002/index1.heta +++ b/cases/0002/index1.heta @@ -16,6 +16,3 @@ r1 @Reaction {actors: s1 -> p1} := Vmax * s1 / (Km + s1) * comp1; // reaction constant Vmax @Const = 0.1; Km @Const = 0.5; - -// export format -#export {format: SBML}; diff --git a/cases/0002/index2.heta b/cases/0002/index2.heta index c7fa4dc..58fbeb9 100644 --- a/cases/0002/index2.heta +++ b/cases/0002/index2.heta @@ -19,6 +19,3 @@ Vmax @Const = 0.1; Km_s1 @Const = 0.5; Km_p1 @Const = 1.1; Keq @Const = 10; - -// export format -#export {format: SBML}; diff --git a/cases/0002/index3.heta b/cases/0002/index3.heta index ac308bc..f5f2314 100644 --- a/cases/0002/index3.heta +++ b/cases/0002/index3.heta @@ -25,6 +25,3 @@ kcat @Const {units: uM/s} = 0.1; Km_s1 @Const {units: uM} = 0.5; Km_p1 @Const {units: uM} = 1.1; Keq @Const {units: UL} = 10; - -// export format -#export {format: SBML}; diff --git a/cases/0002/index4.heta b/cases/0002/index4.heta index ac86627..b06d3a5 100644 --- a/cases/0002/index4.heta +++ b/cases/0002/index4.heta @@ -23,6 +23,3 @@ kcat @Const {units: (1e-6 mole)/litre/second} = 0.1; Km_s1 @Const {units: (1e-6 mole)/litre} = 0.5; Km_p1 @Const {units: (1e-6 mole)/litre} = 1.1; Keq @Const {units: dimensionless} = 10; - -// export format -#export {format: SBML}; diff --git a/cases/0002/index5.heta b/cases/0002/index5.heta index 8067fc5..520c0d5 100644 --- a/cases/0002/index5.heta +++ b/cases/0002/index5.heta @@ -30,6 +30,3 @@ kcat @Const {units: uM/s} = 0.1; Km_s1 @Const {units: uM} = 0.5; Km_p1 @Const {units: uM} = 1.1; Keq @Const {units: UL} = 10; - -// export format -#export {format: SBML}; diff --git a/cases/0003/index0.heta b/cases/0003/index0.heta index a7f5d3c..ae32c1e 100644 --- a/cases/0003/index0.heta +++ b/cases/0003/index0.heta @@ -14,6 +14,3 @@ r1 @Reaction {actors: => m1} := vsyn; // parameters vsyn @Const = 0.1; - -// export -#export {format: SBML}; diff --git a/package-lock.json b/package-lock.json index 753166c..9da5073 100644 --- a/package-lock.json +++ b/package-lock.json @@ -6,7 +6,8 @@ "": { "dependencies": { "glob": "^10.4.1", - "heta-compiler": "^0.8.3" + 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"https://registry.npmjs.org/universalify/-/universalify-2.0.1.tgz", @@ -2220,6 +2549,11 @@ "defaults": "^1.0.3" } }, + "web-streams-polyfill": { + "version": "3.3.3", + "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.3.3.tgz", + "integrity": "sha512-d2JWLCivmZYTSIoge9MsgFCZrt571BikcWGYkjC1khllbTeDlGqZ2D8vD8E/lJa8WGWbb7Plm8/XJYV7IJHZZw==" + }, "webidl-conversions": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz", diff --git a/package.json b/package.json index 2bdf88f..985ed7e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,7 @@ { "dependencies": { "glob": "^10.4.1", - "heta-compiler": "^0.8.3" + "heta-compiler": "^0.8.3", + "openai": "^4.51.0" } } diff --git a/test/sbml-cases.js b/test/sbml-cases.js new file mode 100644 index 0000000..3555ed3 --- /dev/null +++ b/test/sbml-cases.js @@ -0,0 +1,25 @@ +// project level KEYS +// my-service-account openai-test +// setx OPENAI_API_KEY "sk-my-service-account-I1zZPhGR2Byyk4fYHeS8T3BlbkFJ1ccT1hCLQqLBnX1xKb51" + +const { OpenAI } = require('openai'); + +const openai = new OpenAI({ + organization: "org-V73x0GwuiyLqNseJ9DOyGMjy", + project: "proj_tSNHinT8kJJl8LMqqG8X7HQp", + apiKey: "sk-my-service-account-I1zZPhGR2Byyk4fYHeS8T3BlbkFJ1ccT1hCLQqLBnX1xKb51" +}); + +async function main() { + const completion = await openai.completions.create({ + model: 'ft:davinci-002:personal:siple-heta:9alRfxFv', // davinci-002, gpt-3.5-turbo-instruct, babbage-002, ft:davinci-002:personal:sbml-heta:9ZOUT9dV + //prompt: "What is the capital of the United Kingdom?", + prompt: `Create Heta model with stoichiometry 1A + 2D <=> 3C + 4F. No export.`, + max_tokens: 1024, + temperature: 0.1, + }); + console.log(completion.choices[0].text); +} +main(); + +//console.log(openai); \ No newline at end of file