GUI: connectivity tab key coverage

[chenghuzi]

I'm not very familiar with the current parameter file data structure so this might be a dumb question. Currently the connectivity tab is generated by the following keys in parameter files:

    # Sliders to change local-connectivity params
    sliders = [
        _get_sliders(params, [
            'gbar_L2Pyr_L2Pyr_ampa', 'gbar_L2Pyr_L2Pyr_nmda',
            'gbar_L2Basket_L2Pyr_gabaa', 'gbar_L2Basket_L2Pyr_gabab'
        ]),
        _get_sliders(params, [
            'gbar_L2Pyr_L5Pyr', 'gbar_L2Basket_L5Pyr', 'gbar_L5Pyr_L5Pyr_ampa',
            'gbar_L5Pyr_L5Pyr_nmda', 'gbar_L5Basket_L5Pyr_gabaa',
            'gbar_L5Basket_L5Pyr_gabab'
        ]),
        _get_sliders(params,
                     ['gbar_L2Pyr_L2Basket', 'gbar_L2Basket_L2Basket']),
        _get_sliders(params, ['gbar_L2Pyr_L5Pyr', 'gbar_L2Basket_L5Pyr'])
    ]

It seems there're some overlapping keys like gbar_L2Pyr_L5Pyr and gbar_L2Basket_L5Pyr. I'm not sure if this is by design.

Also, I checked default.json, in which we have 15 parameters that seem to relate to connectivity:

    "gbar_L2Pyr_L2Pyr_ampa": 0.0005,
    "gbar_L2Pyr_L2Pyr_nmda": 0.0005,
    "gbar_L2Basket_L2Pyr_gabaa": 0.05,
    "gbar_L2Basket_L2Pyr_gabab": 0.05,
    "gbar_L2Pyr_L5Pyr": 0.00025,
    "gbar_L2Basket_L5Pyr": 0.001,
    "gbar_L5Pyr_L5Pyr_ampa": 0.0005,
    "gbar_L5Pyr_L5Pyr_nmda": 0.0005,
    "gbar_L5Basket_L5Pyr_gabaa": 0.025,
    "gbar_L5Basket_L5Pyr_gabab": 0.025,
    "gbar_L2Pyr_L2Basket": 0.0005,
    "gbar_L2Basket_L2Basket": 0.02,
    "gbar_L2Pyr_L5Basket": 0.00025,
    "gbar_L5Pyr_L5Basket": 0.0005,
    "gbar_L5Basket_L5Basket": 0.02,

Among those gbar_L2Pyr_L5Basket, gbar_L5Pyr_L5Basket and gbar_L5Basket_L5Basket are missing. Should we ignore them or add them to the connectivity tab?

[jasmainak]

You should definitely remove the overlapping keys and add the ones that are missing :) Thanks for catching them! I made the prototype in a week, so some corners were cut ...

[chenghuzi]

No problem. I found that in network_models.py we have a procedure of adding connectivities:

    # ...
    net = Network(params, add_drives_from_params=add_drives_from_params)

    delay = net.delay

    # source of synapse is always at soma

    # layer2 Pyr -> layer2 Pyr
    # layer5 Pyr -> layer5 Pyr
    lamtha = 3.0
    loc = 'proximal'
    for target_cell in ['L2_pyramidal', 'L5_pyramidal']:
        for receptor in ['nmda', 'ampa']:
            key = f'gbar_{_short_name(target_cell)}_'\
                  f'{_short_name(target_cell)}_{receptor}'
            weight = net._params[key]
            net.add_connection(
                target_cell, target_cell, loc, receptor, weight,
                delay, lamtha, allow_autapses=False)

    # layer2 Basket -> layer2 Pyr
    src_cell = 'L2_basket'
    target_cell = 'L2_pyramidal'
    lamtha = 50.
    loc = 'soma'
    for receptor in ['gabaa', 'gabab']:
        key = f'gbar_L2Basket_L2Pyr_{receptor}'
        weight = net._params[key]
        net.add_connection(
            src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    # layer5 Basket -> layer5 Pyr
    src_cell = 'L5_basket'
    target_cell = 'L5_pyramidal'
    lamtha = 70.
    loc = 'soma'
    for receptor in ['gabaa', 'gabab']:
        key = f'gbar_L5Basket_{_short_name(target_cell)}_{receptor}'
        weight = net._params[key]
        net.add_connection(
            src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    # layer2 Pyr -> layer5 Pyr
    src_cell = 'L2_pyramidal'
    lamtha = 3.
    receptor = 'ampa'
    for loc in ['proximal', 'distal']:
        key = f'gbar_L2Pyr_{_short_name(target_cell)}'
        weight = net._params[key]
        net.add_connection(
            src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    # layer2 Basket -> layer5 Pyr
    src_cell = 'L2_basket'
    lamtha = 50.
    key = f'gbar_L2Basket_{_short_name(target_cell)}'
    weight = net._params[key]
    loc = 'distal'
    receptor = 'gabaa'
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    # xx -> layer2 Basket
    src_cell = 'L2_pyramidal'
    target_cell = 'L2_basket'
    lamtha = 3.
    key = f'gbar_L2Pyr_{_short_name(target_cell)}'
    weight = net._params[key]
    loc = 'soma'
    receptor = 'ampa'
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    src_cell = 'L2_basket'
    lamtha = 20.
    key = f'gbar_L2Basket_{_short_name(target_cell)}'
    weight = net._params[key]
    loc = 'soma'
    receptor = 'gabaa'
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    # xx -> layer5 Basket
    src_cell = 'L5_basket'
    target_cell = 'L5_basket'
    lamtha = 20.
    loc = 'soma'
    receptor = 'gabaa'
    key = f'gbar_L5Basket_{_short_name(target_cell)}'
    weight = net._params[key]
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha,
        allow_autapses=False)

    src_cell = 'L5_pyramidal'
    lamtha = 3.
    key = f'gbar_L5Pyr_{_short_name(target_cell)}'
    weight = net._params[key]
    loc = 'soma'
    receptor = 'ampa'
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    src_cell = 'L2_pyramidal'
    lamtha = 3.
    key = f'gbar_L2Pyr_{_short_name(target_cell)}'
    weight = net._params[key]
    loc = 'soma'
    receptor = 'ampa'
    net.add_connection(
        src_cell, target_cell, loc, receptor, weight, delay, lamtha)

    return net

Does this completely add all possible connections? If so I can just port this to a new method in gui.py.

Also, I have two other questions:

1. do 15 connectivity parameter keys in default.json form a complete list of all possible connections?
2. will all future parameter files include all possible connections? If not we need to consider None cases in adding connections

[jasmainak]

1. Actually, look at jones_2009_model. That gives you a complete list of all possible connections.

2. If a parameter file does not include certain connections, then I would say throw an error saying it's not a valid parameter file of jones_2009_model and the error should specify what connections are not specified.

[chenghuzi]

• Actually, look at jones_2009_model. That gives you a complete list of all possible connections

OK I'll use that one.
.

• If a parameter file does not include certain connections, then I would say throw an error saying it's not a valid parameter file of jones_2009_model and the error should specify what connections are not specified.

Sure