https://staging.physiomeproject.org/workspace/64f en-us Hodgkin & Huxley (1952) model This workspace holds a CellML encoding of the Hodgkin & Huxley (1952) model. Add open channel IV of HH models; Add simulation and plot python scripts https://staging.physiomeproject.org/workspace/64f/@@file/ab2962b8796666ad9938a2577611c954f006b5fd Add open channel IV of HH models; Add simulation and plot python scripts WeiweiAi 2022-03-31 Revert Acap to 0.3 https://staging.physiomeproject.org/workspace/64f/@@file/9d4fea2a1b0b60f3c636a2acd2a3c0400c93a8d7 Revert Acap to 0.3 WeiweiAi 2022-03-22 Expose Ag https://staging.physiomeproject.org/workspace/64f/@@file/0958e2e4067a1ca23a31f33c939db300b9c10572 Expose Ag WeiweiAi 2022-03-18 Expose states of gating https://staging.physiomeproject.org/workspace/64f/@@file/4cfd719d6472266926d77e1849c7add13b9de8e8 Expose states of gating WeiweiAi 2022-03-18 Add other parameter print out in the gate_ss; The current setting gives around 20 mV peak of AP, it seems that the m gate doesn't open fast enough. https://staging.physiomeproject.org/workspace/64f/@@file/7afd99617b3d38378c96a34888a5321593b3bef2 Add other parameter print out in the gate_ss; The current setting gives around 20 mV peak of AP, it seems that the m gate doesn't open fast enough. WeiweiAi 2022-03-18 Move the folders to BG; Add open channel testing https://staging.physiomeproject.org/workspace/64f/@@file/f60338fb964a811a3c12944d752e3b0f5165ce39 Move the folders to BG; Add open channel testing WeiweiAi 2022-03-17 Add the testing model for gating process https://staging.physiomeproject.org/workspace/64f/@@file/a5985fb7e709cb1c712d71f565caf70764257052 Add the testing model for gating process WeiweiAi 2022-03-09 update cellLib https://staging.physiomeproject.org/workspace/64f/@@file/b6c5fb47e3f49b1488396447f39d6b7a6cfd01af update cellLib WeiweiAi 2022-03-08 channelX connected with Se; https://staging.physiomeproject.org/workspace/64f/@@file/c389283415195575fb6b1c4ac699501404cde971 channelX connected with Se; The sum of initial values of channel states should be the number of the channels; Modify the scripts to save csv files for documentation; Change matrix.xlsx to csv WeiweiAi 2022-03-08 correct leakage equations; adjust the cost function of gate fiitting process https://staging.physiomeproject.org/workspace/64f/@@file/a617f7cad6bf75496162c76e248d9e1644be7535 correct leakage equations; adjust the cost function of gate fiitting process WeiweiAi 2022-02-14 Modify the geometry value and gating fitting scripts https://staging.physiomeproject.org/workspace/64f/@@file/2499714ec9ee933bbf88810256b04a0a0d191c21 Modify the geometry value and gating fitting scripts Add paras WeiweiAi 2022-02-09 Edit to reproduce the Figure 21 in Physiom paper https://staging.physiomeproject.org/workspace/64f/@@file/839196053ae667fe000d52026a1bc5407f8d7e08 Edit to reproduce the Figure 21 in Physiom paper WeiweiAi 2021-12-14 Add BG params related scripts and matrix https://staging.physiomeproject.org/workspace/64f/@@file/bd02dedb491faf9960ccd23496c19ccd3e339db1 Add BG params related scripts and matrix WeiweiAi 2021-11-24 update plot and fit functions https://staging.physiomeproject.org/workspace/64f/@@file/dba6ceca9a52848cc2bd4b4eda686a814dac2d58 update plot and fit functions WeiweiAi 2021-11-16 Modify the option and layout of plots https://staging.physiomeproject.org/workspace/64f/@@file/33ec3acb84c3155258d02bb680033a714882636e Modify the option and layout of plots WeiweiAi 2021-11-15 Move figure creation outside of the function https://staging.physiomeproject.org/workspace/64f/@@file/4014d7d93ea1ef758966dbcfd1859e3950465a46 Move figure creation outside of the function WeiweiAi 2021-11-15 Update cellLib for the gate_plot.m https://staging.physiomeproject.org/workspace/64f/@@file/e5b790e74a8bdec81933e6bb2716ae9c0a446d34 Update cellLib for the gate_plot.m WeiweiAi 2021-11-15 Update cellLib https://staging.physiomeproject.org/workspace/64f/@@file/3a4b58aa4683b94b7c9e98556dde463d810f1647 Update cellLib WeiweiAi 2021-11-15 Add leakage current https://staging.physiomeproject.org/workspace/64f/@@file/b491530918385a691af78cb7e152c27c706dc4b5 Add leakage current WeiweiAi 2021-11-04 Add BG version of IK and INa https://staging.physiomeproject.org/workspace/64f/@@file/4245a4ee803f37730cd395ea5670890bca5d1e6e Add BG version of IK and INa WeiweiAi 2021-11-03 update gating modules https://staging.physiomeproject.org/workspace/64f/@@file/56477a4817997eaaff1c22e44e31024e69701c02 update gating modules WeiweiAi 2021-11-03 Update IX_BG https://staging.physiomeproject.org/workspace/64f/@@file/08e35c5898bf635a848596751910ede5fdf06b4d Update IX_BG WeiweiAi 2021-11-03 Update the submodule that correction was made for the channelX_BG https://staging.physiomeproject.org/workspace/64f/@@file/c4ec296bd608e3c240460127fa17bd29b517a230 Update the submodule that correction was made for the channelX_BG WeiweiAi 2021-11-03 remove Shelley's unit file module and update cellLib with BG modules https://staging.physiomeproject.org/workspace/64f/@@file/52d7335e6bd041cbc255607d46e50ecd5d0bc8f8 remove Shelley's unit file module and update cellLib with BG modules WeiweiAi 2021-11-03 Add the submodule of units for BG https://staging.physiomeproject.org/workspace/64f/@@file/416de30875134df12e9db1e916941827fa2c2c23 Add the submodule of units for BG WeiweiAi 2021-10-27 Add activation_function.cell, gating_experiment.cell and gating_experiment.sedml to simulate activation function and tau as function of V; https://staging.physiomeproject.org/workspace/64f/@@file/d9231655dc622ff60e69257b731e809923e8c02c Add activation_function.cell, gating_experiment.cell and gating_experiment.sedml to simulate activation function and tau as function of V; Modify and add more plot scripts and figures for Physiome articles WeiweiAi 2021-08-10 Add I_i to stimulated.cellml and outputs; https://staging.physiomeproject.org/workspace/64f/@@file/49fe31141705e19ab6c25163ad5926d37af251f2 Add I_i to stimulated.cellml and outputs; Ajust previous plot scripts and figures for Physiom paper. Add current stimulation and V=0 simulation plot scripts and figures for Physiom paper. Update protocols in cellLib WeiweiAi 2021-08-02 Modify the model to reflect the rearrangement of the library https://staging.physiomeproject.org/workspace/64f/@@file/7235a08d517ef4740ffc45578ab6f5918b962d3c Modify the model to reflect the rearrangement of the library WeiweiAi 2021-07-27 1. Move phiT to the gating_kinetics; https://staging.physiomeproject.org/workspace/64f/@@file/eb2aeec4e8d211b62d370fd78bd1fa1174bb13ab 1. Move phiT to the gating_kinetics; 2. Add time constant (time_const) in the model gate_steady; 3. Import cellLib to reuse the modules unit, time, gating_kinetics, phiT (temperature_factor), protocols, etc 4. Move units, time, temperature_factor (renamed to phiT), periodic-IStim-protocol, Voltage_ramp_protocol, gating-variable and gate_steady to cellLib WeiweiAi 2021-07-27 fixed a typo. https://staging.physiomeproject.org/workspace/64f/@@file/9deb37f114ec618833d71fccb4d7186c7a208161 fixed a typo. WeiweiAi 2021-05-19 add ignore file https://staging.physiomeproject.org/workspace/64f/@@file/d64818ee430b719371857d1c2ac48d8745259b33 add ignore file WeiweiAi 2021-05-19 tidy up the documentation https://staging.physiomeproject.org/workspace/64f/@@file/852bfdc871eedf1ea7add70caa0c06a832452c99 tidy up the documentation WeiweiAi 2021-05-19 Remove the irrelevant folders and files inherited from the original workspace https://staging.physiomeproject.org/workspace/64f/@@file/4e9c4e3c1f9a91b6fcbe2c80d5205aa32ba7e240 Remove the irrelevant folders and files inherited from the original workspace Remove the absolute paths in the *sim.py. WeiweiAi 2021-05-11 Add model status; https://staging.physiomeproject.org/workspace/64f/@@file/2c02c6188a52bd5de019cfdb595024295688f30a Add model status; Fixed the errors in the top level documents. WeiweiAi 2021-05-11 Add titles for the low level documents; https://staging.physiomeproject.org/workspace/64f/@@file/dac7e0c128179c022fede487faa25cb9a7946369 Add titles for the low level documents; Fixed some bad links. WeiweiAi 2021-05-11 Since include is not supported by the PMR, delete readme.rst; https://staging.physiomeproject.org/workspace/64f/@@file/5074b763ad9025abb3013f3983e690e48bfd90e5 Since include is not supported by the PMR, delete readme.rst; Modify the relative paths in README.rst because it will be placed at the top level in the workspace by the server. Since :numref: and :ref: are not supported by the PMR, change them to footnote and implicit hyperlink target. WeiweiAi 2021-05-11 Add readme.rst at the top level to resolve the relative path issue. https://staging.physiomeproject.org/workspace/64f/@@file/b05905c1739d98b1712b1a644d615c6fc0b4a59a Add readme.rst at the top level to resolve the relative path issue. WeiweiAi 2021-05-11 Edit README.rst https://staging.physiomeproject.org/workspace/64f/@@file/c6437d2501a44fea5711d05c0f2c6aeb3903897e Edit README.rst WeiweiAi 2021-05-11 Add documentation for the folders https://staging.physiomeproject.org/workspace/64f/@@file/88ccc81e951da6f376e738b986b9f8d9a589abd9 Add documentation for the folders WeiweiAi 2021-05-11 Add simulated figures https://staging.physiomeproject.org/workspace/64f/@@file/a46b2caf314b3023185c2e8f5da92a12fa3cc3d0 Add simulated figures WeiweiAi 2021-05-11 simplify the documentation structure https://staging.physiomeproject.org/workspace/64f/@@file/3aa535ae990fdae6b8d960471d354aedac6f7739 simplify the documentation structure WeiweiAi 2021-05-11 Add temperature documentation https://staging.physiomeproject.org/workspace/64f/@@file/b9ab08a28535f8476793cd2cb814e4dd82206b8c Add temperature documentation WeiweiAi 2021-05-11 Edit documentation https://staging.physiomeproject.org/workspace/64f/@@file/48827c0892194dd9f203f81fe892afe824da6122 Edit documentation WeiweiAi 2021-05-10 Add documentation https://staging.physiomeproject.org/workspace/64f/@@file/c177badb5a6ff1ec89413c178ecadb5a2e759a44 Add documentation WeiweiAi 2021-05-10 Derive the data of Fig11 in the original publication; https://staging.physiomeproject.org/workspace/64f/@@file/84588840b9565f4bf506a8846bb9f5735f7f2146 Derive the data of Fig11 in the original publication; Change the plot marks and legends; WeiweiAi 2021-05-10 (1) Add component gate_initials and gate_steady to compute initial values of m, n, and h gates https://staging.physiomeproject.org/workspace/64f/@@file/dcbfc81ad776bc96927e9ebd084619ae2560cdb3 (1) Add component gate_initials and gate_steady to compute initial values of m, n, and h gates (2) Add figures, and data derived from the original paper using Engauge Digitizer; (3) Add sedml files for experimental setup (4) Add python simulation and plot scripts to reproduce the figures WeiweiAi 2021-05-04 Change the unit of T from celsius to kelvin to in line with CellML2.0 spec (but the real temperature unit is still celsius, no need to do conversion when setting the temperature parameter for simulation) https://staging.physiomeproject.org/workspace/64f/@@file/c56e1d0255183a1d725eec025cbe79eeee2c8087 Change the unit of T from celsius to kelvin to in line with CellML2.0 spec (but the real temperature unit is still celsius, no need to do conversion when setting the temperature parameter for simulation) WeiweiAi 2021-04-28 Fixed the unit definition issue https://staging.physiomeproject.org/workspace/64f/@@file/bf9ce5e65cd20494b82713ac1c5cc4b3757e8d9d Fixed the unit definition issue WeiweiAi 2021-04-28 Change the temperature T to 18.5 as stated in the paper. https://staging.physiomeproject.org/workspace/64f/@@file/ee1217d73e4f181e7509248a19c5f4ea8d7ed3b3 Change the temperature T to 18.5 as stated in the paper. WeiweiAi 2021-04-27 Change .xml to cellml; https://staging.physiomeproject.org/workspace/64f/@@file/01b5e3d2e6dd9987f71682214516c78e4dd76916 Change .xml to cellml; Add temperature_factor.cellml and corresponding modification to include tempeature in the model; Add clamped_current.cellml, voltage_clamp_protocol.cellml and voltage_clamp_experiment.cellml to simulate membrance current during voltage clamp ( there is an issue at -10 mV but works fine at other voltage conditions); Add propagated_AP.cellml and AP_propagation_experiment.cellml to simulate propagated action potential (issue: the AP doesn't fall); Add data derived from the figures in the original paper using Engauge Digitizer; WeiweiAi 2021-04-27