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| 875 | } | 875 | } |
| 876 | </style> | 876 | </style> |
| 877 | <section·id="Replaying-Parts-of-a-Simulation"> | 877 | <section·id="Replaying-Parts-of-a-Simulation"> |
| 878 | <h1>Replaying·Parts·of·a·Simulation<a·class="headerlink"·href="#Replaying-Parts-of-a-Simulation"·title="Link·to·this·heading">¶</a></h1> | 878 | <h1>Replaying·Parts·of·a·Simulation<a·class="headerlink"·href="#Replaying-Parts-of-a-Simulation"·title="Link·to·this·heading">¶</a></h1> |
| 879 | <p>When·simulating·a·bio-realistic·network,·cells·will·recieve·synaptic·stimulation·from·both·locally·recurrent·connections·as-well-as·feedforward·connections·from·external·inputs.·Often·when·analyzing·the·results·of·a·full·network·activity·we·would·like·to·know·the·contribution·of·only·a·subset·of·the·synaptic·activity.·For·example,·how·much·does·the·feedforward·synapses,·or·only·recurrent·synapses·between·specific·population·of·cells,·contributed·to·the·simulation·results.·Certain·techniques, | 879 | <p>When·simulating·a·bio-realistic·network,·cells·will·recieve·synaptic·stimulation·from·both·locally·recurrent·connections·as-well-as·feedforward·connections·from·external·inputs.·Often·when·analyzing·the·results·of·a·full·network·activity·we·would·like·to·know·the·contribution·of·only·a·subset·of·the·synaptic·activity.·For·example,·how·much·does·the·feedforward·synapses,·or·only·recurrent·synapses·between·specific·population·of·cells,·contributed·to·the·simulation·results.·Certain·techniques, |
| 880 | like·running·with·only·a·subset·of·the·full·network,·or·using·optogenetic/current-clamping·to·turn·on-off·subpoluations,·can·provide·useful·insights·but·also·not·tell·the·full·story·of·a·network·simulation.</p> | 880 | like·running·with·only·a·subset·of·the·full·network,·or·using·optogenetic/current-clamping·to·turn·on-off·subpoluations,·can·provide·useful·insights·but·also·not·tell·the·full·story·of·a·network·simulation.</p> |
| 881 | <p>Instead·we·can·used·the·BMTK·“replay”·input·module·to·disentangle·subsections·of·a·simulation·activity·from·the·full·network·in·BioNet/biophysically·realistic·simulations.·The·BMTK·“replay”·module·let’s·the·user·take·a·previous·simulation,·and·replay·a·simulation·but·using·only·activity·for·only·a·subset·of·the·synapses.·This·can·be·helpful·in·parameter·tuning·and·optimization,·and·for·very·large·networks·can·provide·an·efficient·manner·to·replay·small·subsets·of·a·full·network.</p> | 881 | <p>Instead·we·can·used·the·BMTK·“replay”·input·module·to·disentangle·subsections·of·a·simulation·activity·from·the·full·network·in·BioNet/biophysically·realistic·simulations.·The·BMTK·“replay”·module·let’s·the·user·take·a·previous·simulation,·and·replay·a·simulation·but·using·only·activity·for·only·a·subset·of·the·synapses.·This·can·be·helpful·in·parameter·tuning·and·optimization,·and·for·very·large·networks·can·provide·an·efficient·manner·to·replay·small·subsets·of·a·full·network.</p> |
| 882 | <div><p><img·alt=" | 882 | <div><p><img·alt="004909301ef64228ac56c50b2948d792"·class="no-scaled-link"·src="_images/disconnected_sim_figure.png"·style="width:·700px;"·/></p> |
| 883 | </div><div·class="nbinput·nblast·docutils·container"> | 883 | </div><div·class="nbinput·nblast·docutils·container"> |
| 884 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[1]: | 884 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[1]: |
| 885 | </pre></div> | 885 | </pre></div> |
| 886 | </div> | 886 | </div> |
| 887 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span>from·bmtk.simulator·import·bionet | 887 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span>from·bmtk.simulator·import·bionet |
| 888 | from·bmtk.analyzer.spike_trains·import·plot_raster | 888 | from·bmtk.analyzer.spike_trains·import·plot_raster |
| 889 | </pre></div> | 889 | </pre></div> |
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| 14 | Instead·we·can·used·the·BMTK·“replay”·input·module·to·disentangle·subsections | 14 | Instead·we·can·used·the·BMTK·“replay”·input·module·to·disentangle·subsections |
| 15 | of·a·simulation·activity·from·the·full·network·in·BioNet/biophysically | 15 | of·a·simulation·activity·from·the·full·network·in·BioNet/biophysically |
| 16 | realistic·simulations.·The·BMTK·“replay”·module·let’s·the·user·take·a·previous | 16 | realistic·simulations.·The·BMTK·“replay”·module·let’s·the·user·take·a·previous |
| 17 | simulation,·and·replay·a·simulation·but·using·only·activity·for·only·a·subset | 17 | simulation,·and·replay·a·simulation·but·using·only·activity·for·only·a·subset |
| 18 | of·the·synapses.·This·can·be·helpful·in·parameter·tuning·and·optimization,·and | 18 | of·the·synapses.·This·can·be·helpful·in·parameter·tuning·and·optimization,·and |
| 19 | for·very·large·networks·can·provide·an·efficient·manner·to·replay·small·subsets | 19 | for·very·large·networks·can·provide·an·efficient·manner·to·replay·small·subsets |
| 20 | of·a·full·network. | 20 | of·a·full·network. |
| 21 | [ | 21 | [004909301ef64228ac56c50b2948d792] |
| 22 | [1]: | 22 | [1]: |
| 23 | from·bmtk.simulator·import·bionet | 23 | from·bmtk.simulator·import·bionet |
| 24 | from·bmtk.analyzer.spike_trains·import·plot_raster | 24 | from·bmtk.analyzer.spike_trains·import·plot_raster |
| 25 | *\x8**\x8**\x8**\x8**\x8*·I\x8In\x8ni\x8it\x8ti\x8ia\x8al\x8l·S\x8Si\x8im\x8mu\x8ul\x8la\x8at\x8ti\x8io\x8on\x8n·(\x8(G\x8Ge\x8en\x8ne\x8er\x8ra\x8at\x8ti\x8in\x8ng\x8g·a\x8a·B\x8Ba\x8as\x8se\x8el\x8li\x8in\x8ne\x8e·f\x8fo\x8or\x8r·S\x8Sy\x8yn\x8na\x8ap\x8pt\x8ti\x8ic\x8c·A\x8Ac\x8ct\x8ti\x8iv\x8vi\x8it\x8ty\x8y)\x8)_\x8?\x8¶·*\x8**\x8**\x8**\x8**\x8* | 25 | *\x8**\x8**\x8**\x8**\x8*·I\x8In\x8ni\x8it\x8ti\x8ia\x8al\x8l·S\x8Si\x8im\x8mu\x8ul\x8la\x8at\x8ti\x8io\x8on\x8n·(\x8(G\x8Ge\x8en\x8ne\x8er\x8ra\x8at\x8ti\x8in\x8ng\x8g·a\x8a·B\x8Ba\x8as\x8se\x8el\x8li\x8in\x8ne\x8e·f\x8fo\x8or\x8r·S\x8Sy\x8yn\x8na\x8ap\x8pt\x8ti\x8ic\x8c·A\x8Ac\x8ct\x8ti\x8iv\x8vi\x8it\x8ty\x8y)\x8)_\x8?\x8¶·*\x8**\x8**\x8**\x8**\x8* |
| 26 | First·step·is·to·take·an·existing·network·+·simulation·or·build·one·from | 26 | First·step·is·to·take·an·existing·network·+·simulation·or·build·one·from |
| 27 | scratch.·For·more·information·on·how·to·build·and·run·BioNet·simulations·please | 27 | scratch.·For·more·information·on·how·to·build·and·run·BioNet·simulations·please |
| 28 | see·existing·_\x8t_\x8u_\x8t_\x8o_\x8r_\x8i_\x8a_\x8l_\x8s.·For·our·example·we·copy·the·_\x8b_\x8i_\x8o_\x8n_\x8e_\x8t_\x8__\x84_\x85_\x80_\x8c_\x8e_\x8l_\x8l_\x8·_\x8e_\x8x_\x8a_\x8m_\x8p_\x8l_\x8e | 28 | see·existing·_\x8t_\x8u_\x8t_\x8o_\x8r_\x8i_\x8a_\x8l_\x8s.·For·our·example·we·copy·the·_\x8b_\x8i_\x8o_\x8n_\x8e_\x8t_\x8__\x84_\x85_\x80_\x8c_\x8e_\x8l_\x8l_\x8·_\x8e_\x8x_\x8a_\x8m_\x8p_\x8l_\x8e |