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| 1 | · | 1 | ·f4a67213ca451c28a24bb2f24dcff197·52909360·doc·optional·python3-bmtk-doc_1.1.1+ds-4_all.deb |
| 2 | ·05ba44e5dbe7b33f558b077ecbe91ca7·31021600·python·optional·python3-bmtk-examples_1.1.1+ds-4_all.deb | 2 | ·05ba44e5dbe7b33f558b077ecbe91ca7·31021600·python·optional·python3-bmtk-examples_1.1.1+ds-4_all.deb |
| 3 | ·e8179ed92e1d209a9570ddf4d4615661·532952·python·optional·python3-bmtk_1.1.1+ds-4_amd64.deb | 3 | ·e8179ed92e1d209a9570ddf4d4615661·532952·python·optional·python3-bmtk_1.1.1+ds-4_amd64.deb |
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| 1 | -rw-r--r--···0········0········0········4·2025-02-24·15:24:36.000000·debian-binary | 1 | -rw-r--r--···0········0········0········4·2025-02-24·15:24:36.000000·debian-binary |
| 2 | -rw-r--r--···0········0········0····15104·2025-02-24·15:24:36.000000·control.tar.xz | 2 | -rw-r--r--···0········0········0····15104·2025-02-24·15:24:36.000000·control.tar.xz |
| 3 | -rw-r--r--···0········0········0·5289406 | 3 | -rw-r--r--···0········0········0·52894064·2025-02-24·15:24:36.000000·data.tar.xz |
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| 863 | <span·class="w">···</span><span·class="p">}</span> | 863 | <span·class="w">···</span><span·class="p">}</span> |
| 864 | <span·class="p">}</span> | 864 | <span·class="p">}</span> |
| 865 | </pre></div> | 865 | </pre></div> |
| 866 | </div> | 866 | </div> |
| 867 | <p>To·change·the·stimulus·to·a·WAV·file·of·your·choice,·point·to·the·relative·path·of·the·file·under·“data_file”.</p> | 867 | <p>To·change·the·stimulus·to·a·WAV·file·of·your·choice,·point·to·the·relative·path·of·the·file·under·“data_file”.</p> |
| 868 | <p>The·filter·carrier·consists·of·a·sinusoidal·modulation·in·2D·akin·to·a·plane·wave.·This·carrier·is·multiplied·by·a·Gaussian·envelope·in·the·spectral·axis·and·an·asymmetric·scaled·gamma·distribution·function·in·the·temporal·axis·to·allow·for·faster·onset·of·responses·and·a·slower·tail·decay.</p> | 868 | <p>The·filter·carrier·consists·of·a·sinusoidal·modulation·in·2D·akin·to·a·plane·wave.·This·carrier·is·multiplied·by·a·Gaussian·envelope·in·the·spectral·axis·and·an·asymmetric·scaled·gamma·distribution·function·in·the·temporal·axis·to·allow·for·faster·onset·of·responses·and·a·slower·tail·decay.</p> |
| 869 | <p>Filters·with·very·little·spectral·modulation·have·a·“vertical”·appearance·and·respond·preferentially·to·broadband·temporal·edges·such·as·sound·onsets.·Filters·with·very·little·temporal·modulation·have·a·“horizontal”·appearance·and·respond·preferentially·to·sustained·spectral·edges.·If·the·nodes·are·ordered·by·their·center·frequencies,·we·can·construct·different·“views”·of·the·stimulus·(speech·in·this·case)·through·these·different·types·of·filters.</p> | 869 | <p>Filters·with·very·little·spectral·modulation·have·a·“vertical”·appearance·and·respond·preferentially·to·broadband·temporal·edges·such·as·sound·onsets.·Filters·with·very·little·temporal·modulation·have·a·“horizontal”·appearance·and·respond·preferentially·to·sustained·spectral·edges.·If·the·nodes·are·ordered·by·their·center·frequencies,·we·can·construct·different·“views”·of·the·stimulus·(speech·in·this·case)·through·these·different·types·of·filters.</p> |
| 870 | <div><p><img·alt=" | 870 | <div><p><img·alt="16fa25c914a14457890083616bb177aa"·class="no-scaled-link"·src="_images/Filters_sp_t_mod.png"·style="width:·800px;"·/></p> |
| 871 | </div><p><img·alt="Responses"·src="_images/Responses_to_diff_scales_and_orientations.png"·/></p> | 871 | </div><p><img·alt="Responses"·src="_images/Responses_to_diff_scales_and_orientations.png"·/></p> |
| 872 | <p>Now·we·will·build·a·larger·bank·of·filters·with·randomly·assigned·properties.·Beware·that·if·n_filts·is·set·larger,·the·code·could·take·a·long·time·to·run·in·the·notebook.</p> | 872 | <p>Now·we·will·build·a·larger·bank·of·filters·with·randomly·assigned·properties.·Beware·that·if·n_filts·is·set·larger,·the·code·could·take·a·long·time·to·run·in·the·notebook.</p> |
| 873 | <div·class="nbinput·docutils·container"> | 873 | <div·class="nbinput·docutils·container"> |
| 874 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[3]: | 874 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[3]: |
| 875 | </pre></div> | 875 | </pre></div> |
| 876 | </div> | 876 | </div> |
| 877 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span><span·class="n">n_filts</span>·<span·class="o">=</span>·<span·class="mi">100</span> | 877 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span><span·class="n">n_filts</span>·<span·class="o">=</span>·<span·class="mi">100</span> |
| Offset 138, 15 lines modified | Offset 138, 15 lines modified | ||
| 138 | allow·for·faster·onset·of·responses·and·a·slower·tail·decay. | 138 | allow·for·faster·onset·of·responses·and·a·slower·tail·decay. |
| 139 | Filters·with·very·little·spectral·modulation·have·a·“vertical”·appearance·and | 139 | Filters·with·very·little·spectral·modulation·have·a·“vertical”·appearance·and |
| 140 | respond·preferentially·to·broadband·temporal·edges·such·as·sound·onsets. | 140 | respond·preferentially·to·broadband·temporal·edges·such·as·sound·onsets. |
| 141 | Filters·with·very·little·temporal·modulation·have·a·“horizontal”·appearance·and | 141 | Filters·with·very·little·temporal·modulation·have·a·“horizontal”·appearance·and |
| 142 | respond·preferentially·to·sustained·spectral·edges.·If·the·nodes·are·ordered·by | 142 | respond·preferentially·to·sustained·spectral·edges.·If·the·nodes·are·ordered·by |
| 143 | their·center·frequencies,·we·can·construct·different·“views”·of·the·stimulus | 143 | their·center·frequencies,·we·can·construct·different·“views”·of·the·stimulus |
| 144 | (speech·in·this·case)·through·these·different·types·of·filters. | 144 | (speech·in·this·case)·through·these·different·types·of·filters. |
| 145 | [ | 145 | [16fa25c914a14457890083616bb177aa] |
| 146 | [Responses] | 146 | [Responses] |
| 147 | Now·we·will·build·a·larger·bank·of·filters·with·randomly·assigned·properties. | 147 | Now·we·will·build·a·larger·bank·of·filters·with·randomly·assigned·properties. |
| 148 | Beware·that·if·n_filts·is·set·larger,·the·code·could·take·a·long·time·to·run·in | 148 | Beware·that·if·n_filts·is·set·larger,·the·code·could·take·a·long·time·to·run·in |
| 149 | the·notebook. | 149 | the·notebook. |
| 150 | [3]: | 150 | [3]: |
| 151 | n_filts·=·100 | 151 | n_filts·=·100 |
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| 617 | ··········<div·class="body"·role="main"> | 617 | ··········<div·class="body"·role="main"> |
| 618 | ············ | 618 | ············ |
| 619 | ··<section·id="Replaying-Parts-of-a-Simulation"> | 619 | ··<section·id="Replaying-Parts-of-a-Simulation"> |
| 620 | <h1>Replaying·Parts·of·a·Simulation<a·class="headerlink"·href="#Replaying-Parts-of-a-Simulation"·title="Link·to·this·heading">¶</a></h1> | 620 | <h1>Replaying·Parts·of·a·Simulation<a·class="headerlink"·href="#Replaying-Parts-of-a-Simulation"·title="Link·to·this·heading">¶</a></h1> |
| 621 | <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, | 621 | <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, |
| 622 | 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> | 622 | 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> |
| 623 | <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> | 623 | <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> |
| 624 | <div><p><img·alt="3 | 624 | <div><p><img·alt="383939678f304d76a3f50227f4060cdb"·class="no-scaled-link"·src="_images/disconnected_sim_figure.png"·style="width:·700px;"·/></p> |
| 625 | </div><div·class="nbinput·nblast·docutils·container"> | 625 | </div><div·class="nbinput·nblast·docutils·container"> |
| 626 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[1]: | 626 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[1]: |
| 627 | </pre></div> | 627 | </pre></div> |
| 628 | </div> | 628 | </div> |
| 629 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span><span·class="kn">from</span>·<span·class="nn">bmtk.simulator</span>·<span·class="kn">import</span>·<span·class="n">bionet</span> | 629 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre><span></span><span·class="kn">from</span>·<span·class="nn">bmtk.simulator</span>·<span·class="kn">import</span>·<span·class="n">bionet</span> |
| 630 | <span·class="kn">from</span>·<span·class="nn">bmtk.analyzer.spike_trains</span>·<span·class="kn">import</span>·<span·class="n">plot_raster</span> | 630 | <span·class="kn">from</span>·<span·class="nn">bmtk.analyzer.spike_trains</span>·<span·class="kn">import</span>·<span·class="n">plot_raster</span> |
| 631 | </pre></div> | 631 | </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 | [3 | 21 | [383939678f304d76a3f50227f4060cdb] |
| 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 |