hicsail/constellation-js

Library for combinatorially specifying, constraining, and exploring genetic design spaces.

constellation-js's Issues

sbol generator should query SBH for existing iGem parts

https://synbiohub.org/public/igem/igem_collection/1

Implement categories better

Inputting 'cds', 'CDS', 'coding-sequence' and 'coding_sequence' all generate different results. Currently only 'CDS' will show the correct sbol symbol in D3.

Run through webpack to see what works on just client side

incorporate visbol into UI

use visbol to display the generated sbol

Update documentation to reflect new changes

Document changes from a05f6dc

No errors are thrown when operators are misspelled

promoter thne one-o-more (cds o ribosomeBindingSite) then terminator does not throw an error

designEnumeration doesn't work with zero-or-more

Doesn't occur when node isn't in categories since it throws an error before path[1] is accessed.

Publish package to npm

replace graph lib and replace with d3

We are currently using go.js and do not have a license for the full version, thus leaving a water mark.
While this was easy to use to create a working demo, we should replace it with D3.

Ibis: implement graph intersection for AND

Change front-end so specification only allows SBOL parts

one-or-more (zero-or-more atom) is wrong

Change internal representation of graph to adjacency list

Use IGEM's standard parts registry as categories

API at http://parts.igem.org/Registry_API

write algorithm to untangle nodes in display

Edges and nodes are currently tangled in one another making it difficult to understand their relationships.

The goal is to display them in a manner where they are naturally spread out.

One approach would be to use force-directed drawing algorithms.
D3 already has an example of this: https://bl.ocks.org/mbostock/4062045

Since we are moving to D3 anyway, it probably makes most sense to use the example above.

Ideally, the nodes would look more like this:

add comments and documentation

Parts should be shown on edges and not on nodes

Multiple atoms without operators are treated as one atom

Inputting cds rbs is parsed as cds.
Should throw an error instead since an operator is missing

add linting for style consistency

Connect puppeteer front-end to ibis

Throw error for all undefined categories

Currently only throws an error for the first undefined category it finds
Could be useful to show all categories that are not defined

Bug: extraneous accept state occasionally added to zero-or-more

encompasses zero-or-more / one-or-more

Comment D3 code

Some badly formed inputs don't work but don't throw errors either

For example promoter then $cds then rbs

Update dependencies in package.json

add more descriptive error messages

Demo specification doesn't work with tabs

Can't parse specification when tabs are used

Improve D3 performance

Maybe https://github.com/vasturiano/force-graph

Ibis: traverse graph and enumerate designs

traverse every possible path within graph.
print text representation of paths.

Optimize design shuffling

-Look into reservoir sampling

integrate w/ Travis CI

Generate sbol from constellation output

write unit tests for graph generation

Write unit tests covering cases for:

Binary operators (or, and, then):

• Multiple leaves
• Multiple roots
• Leaf and root

Unary operators (one-or-more, zero-or-more):

• Multiple leaves
• Leaf and root

Document input and correct output for each

enhance UI of graph representation

Nodes:

• Root node: white circle
• Accept node: green circle
• Leaf node: text (no change)

Edges:

• Forward: straight arrow (no change)
• Backward: curved arrow

Split constellation up into UI and actual library

Integrate Constellation with Knox

style index page

Style text box, display box and header. Add description with valid operations

Add cycle detection/handling to design enumeration

encompasses zero-or-more / one-or-more

Ibis: implement function to collapse epsilons

iron out bugs in design enumeration

Restrict keys in categories to terms.js in sboljs

User should not be able to use a key in categories that is not a key in this file

https://github.com/SynBioDex/sboljs/blob/master/lib/terms.js
**ignore sbo and so terms

This list should be referenced directly from sbol.js library so that updates to the list are automatically recognized in Constellation

extend grammar to include syntax used by Mary

Look into simplifying graph generation

Add unit tests to demos

Add UI Boolean for POST request

Ibis: build translation from abstract syntax to graph representation

Client.html broken

Paths to CSS and JS files are incorrect

Fix bugs with commands

Multiple ors broke during refactoring. Seems to be an issue with epsilon nodes not being added
Multiple zero-or-ones seem to be failing due to an edge case with handleZeroOrOne
See unit tests

Update UI to support new cycle features

Redo error handling in the browser