Single, cleaner format for specifying connections #90
Description
Currently many ugly, inconsistent constructs are used for specifying connections:
<projection id="internal2" presynapticPopulation="iafCells" postsynapticPopulation="iafCells" synapse="syn2">
<connection id="0" preCellId="../iafCells/0/iaf" postCellId="../iafCells/2/iaf"/>
</projection>
<projection id="projAMPA" presynapticPopulation="pop0" postsynapticPopulation="pop0" synapse="AMPA">
<connection id="0" preCellId="../pop0/0/MultiCompCell" postCellId="../pop0/1/MultiCompCell" preSegmentId="0" preFractionAlong="0.5" postSegmentId="0" postFractionAlong="0.5"/>
</projection>
<electricalProjection id ="testGJconn" presynapticPopulation="iafPop1" postsynapticPopulation="iafPop2">
<electricalConnectionInstance id="0" preCell="../iafPop1/0/iaf" postCell="../iafPop2/0/iaf" preSegment="0" preFractionAlong="0.5" postSegment="0" postFractionAlong="0.5" synapse="gj1"/>
</electricalProjection>
<continuousProjection id ="testGradedConn" presynapticPopulation="hhPop1" postsynapticPopulation="hhPop2">
<continuousConnectionInstance id="0" preCell="../hhPop1/0/hhcell" postCell="../hhPop2/0/hhcell" preComponent="silent1" postComponent="gs1"/>
</continuousProjection>
Issues can be summarised as:
- Use of "../hhPop1/0/hhcell" etc This is mainly due to restrictions placed by jLEMS on the form of preCellId so that connections can be made between components in jLEMS. See component type definitions for these.
- Inconsistencies in preCellId/preCell The latter form is more consistent with the rest of NeuroML, but the former is older and still in use. See also Old and new format for connections #89
- Need for electricalConnection & electricalConnectionInstance This is due to different definitions of these in the component type definitions.
- synapse specified in each electricalConnectionInstance See synapse should be moved from electricalConnection to electricalProjection #76
- preComponent & postComponent in each continuousConnectionInstance