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aging-research
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species

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  1. select_genes:
    2. 

  2.   cmd: papermill -f stages/1_select_genes_and_species.yaml  --progress-bar --report-mode
    3. 

  3.     notebooks/1_select_genes_and_species.ipynb data/output/notebooks/1_select_genes_and_species_report.ipynb
    4. 

  4.   deps:
    5. 

  5.   - path: data/input/genes/by_animal_class
    6. 

  6.     md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
    7. 

  7.   - path: data/input/samples.tsv
    8. 

  8.     md5: 17e2bb8020c8ac1f8c3c7445fac901c3
    9. 

  9.   - path: data/input/species.tsv
    10. 

  10.     md5: cdf6379f1d78780afc6f650b10636494
    11. 

  11.   - path: notebooks/1_select_genes_and_species.ipynb
    12. 

  12.     md5: 201de29fbe33b8bf5b546fcf16ec15f6
    13. 

  13.   - path: stages/1_select_genes_and_species.yaml
    14. 

  14.     md5: 22f95cba7413c7c641fec0720b8338ee
    15. 

  15.   outs:
    16. 

  16.   - path: data/interim/selected_expressions.tsv
    17. 

  17.     md5: d872ec9f5ff9ac16d7dd6d877cc077b1
    18. 

  18.   - path: data/interim/selected_genes.tsv
    19. 

  19.     md5: dc2b3b921d9fb4ed358a085c53426307
    20. 

  20.   - path: data/interim/selected_samples.tsv
    21. 

  21.     md5: f3a11a4ad6550a7f356bf51e7a4e183b
    22. 

  22.   - path: data/interim/selected_species.tsv
    23. 

  23.     md5: 74a64f77b443ed7b6e9b44240953ec7a
    24. 

  24.   - path: data/output/counts/species_sample_count.tsv
    25. 

  25.     md5: eced40b842c0ec786a43d0e8c1da073d
    26. 

  26.   - path: data/output/counts/species_tissue_sample_count.tsv
    27. 

  27.     md5: 7e78391b84b265bdc0db65ef0f293056
    28. 

  28.   - path: data/output/counts/tissue_sample_count.tsv
    29. 

  29.     md5: 95d7d50886117aae30a8ee8c335f5076
    30. 

  30.   - path: data/output/notebooks/1_select_genes_and_species_report.ipynb
    31. 

  31.     md5: c170a67d0a586c49d1442695c78bdcbc
    32. 

  32. select_samples:
    33. 

  33.   cmd: papermill -f parameters/select_samples.yaml  --progress-bar --report-mode notebooks/select_samples.ipynb
    34. 

  34.     data/output/notebooks/select_samples.ipynb
    35. 

  35.   deps:
    36. 

  36.   - path: data/input/genes/by_animal_class
    37. 

  37.     md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
    38. 

  38.   - path: data/input/samples.tsv
    39. 

  39.     md5: 17e2bb8020c8ac1f8c3c7445fac901c3
    40. 

  40.   - path: data/input/species.tsv
    41. 

  41.     md5: cdf6379f1d78780afc6f650b10636494
    42. 

  42.   - path: data/input/total_mtDNA_base_composition.csv
    43. 

  43.     md5: 3735cfc4beffb6c9356f908525345ee6
    44. 

  44.   - path: notebooks/select_samples.ipynb
    45. 

  45.     md5: 9db059d4bd6319903528a5f737f0f4f0
    46. 

  46.   - path: parameters/select_samples.yaml
    47. 

  47.     md5: ccd2ff9e431a861a3cabaf02eb5533ab
    48. 

  48.   outs:
    49. 

  49.   - path: data/interim/selected/gestation_days
    50. 

  50.     md5: 03f0461ba9a1ca26f052203b948cd78b.dir
    51. 

  51.   - path: data/interim/selected/lifespan
    52. 

  52.     md5: 65f40bf267437f9a07131d706e0fed3d.dir
    53. 

  53.   - path: data/interim/selected/mass_kg
    54. 

  54.     md5: f36dbab9692c98800c464052e8dc85af.dir
    55. 

  55.   - path: data/interim/selected/metabolic_rate
    56. 

  56.     md5: 470ea1aeccc3bafa4b93268181360e6d.dir
    57. 

  57.   - path: data/interim/selected/mtGC
    58. 

  58.     md5: fa17686c777e1fad034b626b1efad921.dir
    59. 

  59.   - path: data/interim/selected/temperature
    60. 

  60.     md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
    61. 

  61.   - path: data/output/counts/species_sample_count.tsv
    62. 

  62.     md5: 84c76b86cb61c5bf73c7f06c390dc064
    63. 

  63.   - path: data/output/counts/species_tissue_sample_count.tsv
    64. 

  64.     md5: e1b7a7f290203cad12f412d33e2a0bcb
    65. 

  65.   - path: data/output/counts/tissue_sample_count.tsv
    66. 

  66.     md5: 5a1441ea61f14d0242037f6a36c9d4a4
    67. 

  67.   - path: data/output/notebooks/select_samples.ipynb
    68. 

  68.     md5: 9180d0511d85cc0c4544dd4930a64b69
    69. 

  69. results_intersections:
    70. 

  70.   cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    71. 

  71.     notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    72. 

  72.   deps:
    73. 

  73.   - path: data/output/external/causality
    74. 

  74.     md5: c00e3428ab5aac19fdc6c5157b09fb33.dir
    75. 

  75.   - path: data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    76. 

  76.     md5: e3cf4199fa5234888c6fe0f388f87426
    77. 

  77.   - path: data/output/external/linear
    78. 

  78.     md5: ccaa8c167006ee5e320c709bfcdc0d6d.dir
    79. 

  79.   - path: data/output/external/shap
    80. 

  80.     md5: fb35c5a65c49be61d7dacdc1fba3764b.dir
    81. 

  81.   - path: parameters/results_intersections.yaml
    82. 

  82.     md5: b1f4e5899bf2548de8a69cb96ce6f192
    83. 

  83.   outs:
    84. 

  84.   - path: data/output/intersections/genage_human_intersections.tsv
    85. 

  85.     md5: 7cd1e7ff10c8e35b41e884f355911437
    86. 

  86.   - path: data/output/intersections/genage_model_intersections.tsv
    87. 

  87.     md5: adaefd5646ae0c275ec680989663ef9c
    88. 

  88.   - path: data/output/intersections/intersections.tsv
    89. 

  89.     md5: d9748c0547ec3c01f122c2a967e6d37e
    90. 

  90.   - path: data/output/intersections/intersections_5_and_7.tsv
    91. 

  91.     md5: 5606ff2b9dd0269104b07509760fb824
    92. 

  92.   - path: data/output/intersections/new_old_comparison.tsv
    93. 

  93.     md5: 440391dfccd04e58897f3bb1c898b74b
    94. 

  94.   - path: data/output/notebooks/results_intersections.ipynb
    95. 

  95.     md5: 4aa03ee3831120e7a7d76ed0351e9a46
    96. 

  96. shap_selection:
    97. 

  97.   cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode notebooks/shap_selection.ipynb
    98. 

  98.     data/output/notebooks/shap_selection.ipynb
    99. 

  99.   deps:
    100. 

  100.   - path: data/interim/selected/gestation_days
    101. 

  101.     md5: 03f0461ba9a1ca26f052203b948cd78b.dir
    102. 

  102.   - path: data/interim/selected/lifespan
    103. 

  103.     md5: 65f40bf267437f9a07131d706e0fed3d.dir
    104. 

  104.   - path: data/interim/selected/mass_kg
    105. 

  105.     md5: f36dbab9692c98800c464052e8dc85af.dir
    106. 

  106.   - path: data/interim/selected/metabolic_rate
    107. 

  107.     md5: 470ea1aeccc3bafa4b93268181360e6d.dir
    108. 

  108.   - path: data/interim/selected/mtGC
    109. 

  109.     md5: fa17686c777e1fad034b626b1efad921.dir
    110. 

  110.   - path: data/interim/selected/temperature
    111. 

  111.     md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
    112. 

  112.   - path: parameters/shap_selection.yaml
    113. 

  113.     md5: 43734a0f6f4865a78d36e5ea7e773176
    114. 

  114.   outs:
    115. 

  115.   - path: data/interim/stage_1/results_concatenated.tsv
    116. 

  116.     md5: aed0d7ed5a721fb780f90a2dccbd70e5
    117. 

  117.   - path: data/interim/stage_2/input_data
    118. 

  118.     md5: 9f1ca3ea434625790c4cab969e07aab7.dir
    119. 

  119.   - path: data/output/notebooks/shap_selection.ipynb
    120. 

  120.     md5: c48cb96cd95b4936a3adb043018a6d8c
    121. 

  121.   - path: data/output/plots/stage_one_summary_lifespan.svg
    122. 

  122.     md5: dbe5c9bbbbf06e6a62bf2f447b78010f
    123. 

  123.   - path: data/output/plots/stage_two_untuned_summary_lifespan.svg
    124. 

  124.     md5: f10b432adda8d0ef644b972515cfba24
    125. 

  125. tuning:
    126. 

  126.   cmd: echo "work in progress!"
    127. 

  127.   deps:
    128. 

  128.   - path: data/interim/selected/expressions.tsv
    129. 

  129.     md5: e8e8ea38f54eec4c9d51069d8cc2fde0
    130. 

  130.   - path: data/interim/selected/genes.tsv
    131. 

  131.     md5: 08f457c2517b3f601f5e58e3b1ec4ae0
    132. 

  132.   - path: data/interim/selected/genes_meta.tsv
    133. 

  133.     md5: 0387f21fcd4b287dc924432c8b90042d
    134. 

  134.   - path: data/interim/selected/samples.tsv
    135. 

  135.     md5: c370e925f56a0ed33b7dcb16553d4c39
    136. 

  136.   - path: data/interim/selected/species.tsv
    137. 

  137.     md5: 44e0c63a0d7749abcd43b3c1f92cc54b
    138. 

  138.   outs:
    139. 

  139.   - path: data/output/optimization/study.sqlite
    140. 

  140.     md5: ef8116b0684832e6e11749edcd4e5cbf
    141. 

  141. tune:
    142. 

  142.   cmd: python tune.py
    143. 

  143.   deps:
    144. 

  144.   - path: data/interim/selected/gestation_days
    145. 

  145.     md5: 03f0461ba9a1ca26f052203b948cd78b.dir
    146. 

  146.   - path: data/interim/selected/lifespan
    147. 

  147.     md5: 65f40bf267437f9a07131d706e0fed3d.dir
    148. 

  148.   - path: data/interim/selected/mass_kg
    149. 

  149.     md5: f36dbab9692c98800c464052e8dc85af.dir
    150. 

  150.   - path: data/interim/selected/metabolic_rate
    151. 

  151.     md5: 470ea1aeccc3bafa4b93268181360e6d.dir
    152. 

  152.   - path: data/interim/selected/mtGC
    153. 

  153.     md5: fa17686c777e1fad034b626b1efad921.dir
    154. 

  154.   - path: data/interim/selected/temperature
    155. 

  155.     md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
    156. 

  156.   params:
    157. 

  157.     parameters/tune.yaml:
    158. 

  158.       debug_local: true
    159. 

  159.       folds: 5
    160. 

  160.       hold_outs: 1
    161. 

  161.       metrics: r2_huber_kendall
    162. 

  162.       not_validated_species: true
    163. 

  163.       repeats: 10
    164. 

  164.       threads: 1
    165. 

  165.       trait: lifespan
    166. 

  166.       trials: 10
    167.
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Integrate Google Cloud Storage
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species is now integrated with Google Cloud Storage!

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Use any S3 compatible storage!

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Specify your S3 bucket

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Congratulations!

species is now integrated with your S3 compatible storage!

Delete Storage Key

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Integrate Azure Cloud Storage
Use Azure Storage
Select bucket
Set key
Finish

Use Azure Cloud Storage!

Browsing data directories saved to Azure Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Azure Storage bucket

Access key (If needed)

Congratulations!

species is now integrated with Azure Cloud Storage!

Delete Storage Key

Are you sure you want to delete this access key?

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