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Dataset Open Access

Multi-parameter photon-byphoton hidden Markov modeling dataset

Harris, Paul David; Weiss, Shimon; Lerner, Eitan

The core jupyter notebooks demonstrating mpH2MM using real nsALEX data on DNA hairpin and theRNAP complex with the RPo transcription bubble. Also included are the jupyter notebooks for generating simulated photon trajectories to test the validity of the Integrated complete likelihood (ICL) on data where the ground truth is known.

Included are all HDF5 files used by the jupyter notebooks, as well as .csv files containing all H2MM models generated during the processing of the data.

Files (347.8 MB)
Name Size
1. Simulate 3D trajectories - 600s.ipynb
md5:e5db81b43c6e405e6da55b80bc66a247
334.0 kB Download
2. Generate static smFRET data - 600s.ipynb
md5:2d02fdf13e9068fa5617832d8da215e7
4.4 MB Download
3. Two states smFRET simulation - 600s.ipynb
md5:bfa92a313cb73f55319b0ae328fc010d
38.4 kB Download
4-ICL-SimulatedData.ipynb
md5:8994e2a92aa9147d5fda79d067e11853
21.5 MB Download
H2MM-Multidimensional-Example-PIE_HP3_TE100_SPC630-AutoChoose-ICL-nanotime.ipynb
md5:ceec52bcd672dc4ce510de98c8c4d970
1.8 MB Download
H2MM-Multidimensional-Example-PIE_HP3_TE200_SPC630-AutoChoose-ICL-nanotime.ipynb
md5:af21d4417baf6810a33f5230fb293326
1.9 MB Download
H2MM-Multidimensional-Example-PIE_HP3_TE300_SPC630-AutoChoose-ICL-nanotime.ipynb
md5:d634a748a13e2880f181fba7f8df61ff
2.2 MB Download
H2MM-Multidimensional-Example-PIE_HP3_TE350_SPC630-AutoChoose-ICL-nanotime.ipynb
md5:7482e65c8216146a1cce007050e867c6
2.2 MB Download
H2MM-Multidimensional-Example-PIE_HP3_TE50_SPC630-AutoChoose-ICL-nanotime.ipynb
md5:c204240662a5c74f77de84417f8a9bdd
1.8 MB Download
H2MM-Multidimensional-Example-PIE_minus8TA_minus6NTD_Free-AutoChoose-ICL-nanotime.ipynb
md5:e3dee9e262945faac23440bbec8bb71a
2.0 MB Download
H2MM-Multidimensional-Example-PIE_minus8TA_minus6NTD_RPo-AutoChoose-ICL-nanotime.ipynb
md5:e4d0c08e07e9c3fd2117f09845f31cdd
2.4 MB Download
HP3_TE100_SPC630.hdf5
md5:9464e5ac59abfddef0d2d0b415bd0fee
20.3 MB Download
HP3_TE100_SPC630_da_models.csv
md5:888bf560f314e91fd43887f3d5c6e764
4.6 kB Download
HP3_TE200_SPC630.hdf5
md5:29116acec17929ad26811b71e2f8650e
34.1 MB Download
HP3_TE200_SPC630_da_models.csv
md5:ebf278db4783ac2ade995e09936c1d14
4.6 kB Download
HP3_TE300_SPC630.hdf5
md5:86ce338bbbf4e484e88ad20e83f4098d
45.7 MB Download
HP3_TE300_SPC630_da_models.csv
md5:b8f01e4f22aa4d08b8ff675f177249ca
6.0 kB Download
HP3_TE350_SPC630.hdf5
md5:32865642d1b951517783e782df1a9d82
44.2 MB Download
HP3_TE350_SPC630_da_models.csv
md5:72e95818874d3fd1560c41247dd6be87
6.0 kB Download
HP3_TE50_SPC630.hdf5
md5:5acf88ef689e75f0a055e4de4e83d568
26.4 MB Download
HP3_TE50_SPC630_da_models.csv
md5:e888d8de5e37df0051eb39220c736f86
4.6 kB Download
minus8ta_minus6ntd_free_rt_1.hdf5
md5:c73ef7e450947e83736f0e8893b3008e
25.2 MB Download
minus8ta_minus6ntd_free_rt_1_da_models.csv
md5:04e99895d934960d439020c1852b11a0
6.0 kB Download
minus8ta_minus6ntd_rpo_rt_1.hdf5
md5:fd2d63eae27bd37629f7181e43f1f9e8
90.6 MB Download
minus8ta_minus6ntd_rpo_rt_1_da_models.csv
md5:14a1109b83215c2bef7610e5129802fa
6.0 kB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau100-100us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:9cc7cb610f79601e6c00153fe217cece
3.4 MB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau1000-500us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:766e1c31db119a1cfcb233c100c36824
3.5 MB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau20-10us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:17fcec471725ad6b677e62586e4a9e24
3.5 MB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau400-200us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:1eff2dedccf32b9bac31b6d403ae22dc
3.5 MB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau400-400us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:b32cb3c13f90dbe1db112cdb3fac4650
3.4 MB Download
smFRET_0eb9b3_P_35_s0_D_2.5e-11_dynamics_E_40-75_Tau800-400us_EmTot_226k-200k_BgD900_BgA600_t_max_600s.hdf5
md5:761606cefada1bf20562285c78dde571
3.5 MB Download
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