Skip to content

Commit 82299d7

Browse files
pwrosepwrose
committed
updated rule numbers
1 parent bf86096 commit 82299d7

19 files changed

+610
-598
lines changed

‎README.md‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ This example demonstrates a reproducible 4-step workflow for predicting a protei
1111

1212
---
1313

14-
**Rule 8: Expect Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a non-interactive preview of notebooks and ![Binder](https://mybinder.org/badge.svg) buttons launch
14+
**Rule 9: Enable Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a non-interactive preview of notebooks and ![Binder](https://mybinder.org/badge.svg) buttons launch
1515
notebooks in your web browser using the Binder ([mybinder.org](https://mybinder.org/)) server (may be slow!). The HTML links provide a permanent static record of the notebooks. All notebooks can also be launched directly from the links in the 0-Workflow.ipynb top-level notebook.
1616

1717
---
@@ -26,7 +26,7 @@ notebooks in your web browser using the Binder ([mybinder.org](https://mybinder.
2626

2727
---
2828

29-
**Rule 7: Share and Explain Your Data.** To enable reproducibility, we provide a example1/data directory with all data required to run the workflow. A description of the data with download location and download date is [available](./example1/data/Datasets.md).
29+
**Rule 8: Share and Explain Your Data.** To enable reproducibility, we provide a example1/data directory with all data required to run the workflow. A description of the data with download location and download date is [available](./example1/data/Datasets.md).
3030

3131
---
3232

‎example1/0-Workflow.html‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -11787,8 +11787,8 @@ <h1 id="Predict-Fold-Type-of-a-Protein-from-Protein-Sequence">Predict Fold Type
1178711787
<p><strong>For example, this notebook demonstrates:</strong></p>
1178811788
<hr>
1178911789
<p><strong>Rule 1: Tell a Story for an Audience.</strong> This notebook was developed to learn how to apply a simple machine learning model to predict protein features based on protein sequences.</p>
11790-
<p><strong>Rule 3: Build a Pipeline.</strong> This notebook describes the entire workflow from data preparation, feature calculation, model fitting, to prediction. The modularity makes it easy to replace one of the steps, for example, use a different method to calculate features or apply a different machine learning model.</p>
11791-
<p><strong>Rule 5: Use Cell, Section and Notebook Divisions to Make Steps Clear.</strong> We broke the workflow into separate notebooks and use this top-level notebook to explain and organize the workflow.</p>
11790+
<p><strong>Rule 3: Add Divisions to Make Steps Clear.</strong> We broke the workflow into separate notebooks and use this top-level notebook to explain and organize the workflow.</p>
11791+
<p><strong>Rule 7: Build a Pipeline.</strong> This notebook describes the entire workflow from data preparation, feature calculation, model fitting, to prediction. The modularity makes it easy to replace one of the steps, for example, use a different method to calculate features or apply a different machine learning model.</p>
1179211792
<hr>
1179311793

1179411794
</div>
@@ -11986,7 +11986,7 @@ <h2 id="Version-and-Hardware-Information">Version and Hardware Information<a cla
1198611986
<div class="inner_cell">
1198711987
<div class="text_cell_render border-box-sizing rendered_html">
1198811988
<hr>
11989-
<p><strong>Rule 6: Declare Dependencies.</strong> Here we use the watermark extension to print software, operating system, and hardware version information.</p>
11989+
<p><strong>Rule 5: Record Dependencies.</strong> Here we use the watermark extension to print software, operating system, and hardware version information.</p>
1199011990
<hr>
1199111991

1199211992
</div>

‎example1/0-Workflow.ipynb‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,9 +19,11 @@
1919
"\n",
2020
"**Rule 1: Tell a Story for an Audience.** This notebook was developed to learn how to apply a simple machine learning model to predict protein features based on protein sequences.\n",
2121
"\n",
22-
"**Rule 3: Build a Pipeline.** This notebook describes the entire workflow from data preparation, feature calculation, model fitting, to prediction. The modularity makes it easy to replace one of the steps, for example, use a different method to calculate features or apply a different machine learning model.\n",
22+
"**Rule 3: Add Divisions to Make Steps Clear.** We broke the workflow into separate notebooks and use this top-level notebook to explain and organize the workflow.\n",
23+
"\n",
24+
"**Rule 7: Build a Pipeline.** This notebook describes the entire workflow from data preparation, feature calculation, model fitting, to prediction. The modularity makes it easy to replace one of the steps, for example, use a different method to calculate features or apply a different machine learning model.\n",
25+
"\n",
2326
"\n",
24-
"**Rule 5: Use Cell, Section and Notebook Divisions to Make Steps Clear.** We broke the workflow into separate notebooks and use this top-level notebook to explain and organize the workflow.\n",
2527
"\n",
2628
"---"
2729
]
@@ -186,7 +188,7 @@
186188
"source": [
187189
"---\n",
188190
"\n",
189-
"**Rule 6: Declare Dependencies.** Here we use the watermark extension to print software, operating system, and hardware version information.\n",
191+
"**Rule 5: Record Dependencies.** Here we use the watermark extension to print software, operating system, and hardware version information.\n",
190192
"\n",
191193
"---"
192194
]

‎example1/1-CreateDataset.html‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -11785,9 +11785,9 @@ <h1 id="Create-Dataset">Create Dataset<a class="anchor-link" href="#Create-Datas
1178511785
<div class="inner_cell">
1178611786
<div class="text_cell_render border-box-sizing rendered_html">
1178711787
<hr>
11788-
<p><strong>Rule 2: Document Process, Not Just Results.</strong> Here we describe the steps how to produce the dataset.</p>
11789-
<p><strong>Rule 3: Build a Pipeline.</strong> Besides documenting all steps, the entire process of dataset creation from the original data files in the /data directory is automated. There are no manual steps.</p>
11790-
<p><strong>Rule 7: Share and Explain Your Data.</strong> To enable reproducibility we provide a /data directory with data files and a file that describes the datasets with download locations and dates.</p>
11788+
<p><strong>Rule 2: Document the Process, Not Just the Results.</strong> Here we describe the steps how to produce the dataset.</p>
11789+
<p><strong>Rule 7: Build a Pipeline.</strong> Besides documenting all steps, the entire process of dataset creation from the original data files in the /data directory is automated. There are no manual steps.</p>
11790+
<p><strong>Rule 8: Share and Explain Your Data.</strong> To enable reproducibility we provide a /data directory with data files and a file that describes the datasets with download locations and dates.</p>
1179111791
<hr>
1179211792

1179311793
</div>

‎example1/1-CreateDataset.ipynb‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -13,11 +13,15 @@
1313
"metadata": {},
1414
"source": [
1515
"---\n",
16-
"**Rule 2: Document Process, Not Just Results.** Here we describe the steps how to produce the dataset.\n",
16+
"**Rule 2: Document the Process, Not Just the Results.** Here we describe the steps how to produce the dataset.\n",
17+
"\n",
18+
"\n",
19+
"**Rule 7: Build a Pipeline.** Besides documenting all steps, the entire process of dataset creation from the original data files in the /data directory is automated. There are no manual steps.\n",
20+
"\n",
21+
"\n",
22+
"**Rule 8: Share and Explain Your Data.** To enable reproducibility we provide a /data directory with data files and a file that describes the datasets with download locations and dates.\n",
1723
"\n",
18-
"**Rule 3: Build a Pipeline.** Besides documenting all steps, the entire process of dataset creation from the original data files in the /data directory is automated. There are no manual steps.\n",
1924
"\n",
20-
"**Rule 7: Share and Explain Your Data.** To enable reproducibility we provide a /data directory with data files and a file that describes the datasets with download locations and dates.\n",
2125
"\n",
2226
"---"
2327
]

‎example1/2-CalculateFeatures.html‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11785,9 +11785,9 @@ <h1 id="Calculate-Features">Calculate Features<a class="anchor-link" href="#Calc
1178511785
<div class="inner_cell">
1178611786
<div class="text_cell_render border-box-sizing rendered_html">
1178711787
<hr>
11788+
<p><strong>Rule 3: Add Divisions to Make Steps Clear.</strong> We use one cell for each distinct task.</p>
1178811789
<p><strong>Rule 4: Modularize Code.</strong> To avoid duplicating code, we have collected several functions in protvectors.py. These functions are also used in 4-Predict.</p>
11789-
<p><strong>Rule 5: Use Cell, Section and Notebook Divisions to Make Steps Clear.</strong> We use one cell for each distinct task.</p>
11790-
<p><strong>Rule 7: Share and Explain Your Data.</strong> To enable reproducibility we provide a local copy of a Word2vec model in the /data directory and a file that describes the datasets with download locations and dates.</p>
11790+
<p><strong>Rule 8: Share and Explain Your Data.</strong> To enable reproducibility we provide a local copy of a Word2vec model in the /data directory and a file that describes the datasets with download locations and dates.</p>
1179111791
<hr>
1179211792

1179311793
</div>

‎example1/2-CalculateFeatures.ipynb‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,11 +14,14 @@
1414
"source": [
1515
"---\n",
1616
"\n",
17+
"\n",
18+
"**Rule 3: Add Divisions to Make Steps Clear.** We use one cell for each distinct task.\n",
19+
"\n",
20+
"\n",
1721
"**Rule 4: Modularize Code.** To avoid duplicating code, we have collected several functions in protvectors.py. These functions are also used in 4-Predict.\n",
1822
"\n",
19-
"**Rule 5: Use Cell, Section and Notebook Divisions to Make Steps Clear.** We use one cell for each distinct task.\n",
2023
"\n",
21-
"**Rule 7: Share and Explain Your Data.** To enable reproducibility we provide a local copy of a Word2vec model in the /data directory and a file that describes the datasets with download locations and dates.\n",
24+
"**Rule 8: Share and Explain Your Data.** To enable reproducibility we provide a local copy of a Word2vec model in the /data directory and a file that describes the datasets with download locations and dates.\n",
2225
"\n",
2326
"---"
2427
]

‎example1/3-FitModel.html‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11785,7 +11785,7 @@ <h1 id="Fit-Model">Fit Model<a class="anchor-link" href="#Fit-Model">&#182;</a><
1178511785
<div class="inner_cell">
1178611786
<div class="text_cell_render border-box-sizing rendered_html">
1178711787
<hr>
11788-
<p><strong>Rule 8: Expect Your Notebooks to be Read, Run, and Explored.</strong> We use ipywidgets to present the user with a pull-down menu to select a machine learning model.</p>
11788+
<p><strong>Rule 9: Enable Your Notebooks to Be Read, Run, and Explored.</strong> We use ipywidgets to present the user with a pull-down menu to select a machine learning model.</p>
1178911789
<hr>
1179011790

1179111791
</div>
@@ -12067,13 +12067,13 @@ <h2 id="Select-a-Classification-Method-(default-SVM)">Select a Classification Me
1206712067

1206812068

1206912069

12070-
<div id="72975887-e743-4b27-85e6-5a2193987a6a"></div>
12070+
<div id="7e452311-80e2-4f6d-b442-a3869f7fd770"></div>
1207112071
<div class="output_subarea output_widget_view ">
1207212072
<script type="text/javascript">
12073-
var element = $('#72975887-e743-4b27-85e6-5a2193987a6a');
12073+
var element = $('#7e452311-80e2-4f6d-b442-a3869f7fd770');
1207412074
</script>
1207512075
<script type="application/vnd.jupyter.widget-view+json">
12076-
{"model_id": "ab03394bfe0b457ea53b160d07957fc3", "version_major": 2, "version_minor": 0}
12076+
{"model_id": "c304a2d147484533bca674876ec1235f", "version_major": 2, "version_minor": 0}
1207712077
</script>
1207812078
</div>
1207912079

‎example1/3-FitModel.ipynb‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
"source": [
1515
"---\n",
1616
"\n",
17-
"**Rule 8: Expect Your Notebooks to be Read, Run, and Explored.** We use ipywidgets to present the user with a pull-down menu to select a machine learning model.\n",
17+
"**Rule 9: Enable Your Notebooks to Be Read, Run, and Explored.** We use ipywidgets to present the user with a pull-down menu to select a machine learning model.\n",
1818
"\n",
1919
"---"
2020
]
@@ -249,7 +249,7 @@
249249
{
250250
"data": {
251251
"application/vnd.jupyter.widget-view+json": {
252-
"model_id": "ab03394bfe0b457ea53b160d07957fc3",
252+
"model_id": "c304a2d147484533bca674876ec1235f",
253253
"version_major": 2,
254254
"version_minor": 0
255255
},

‎example1/4-Predict.html‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11785,7 +11785,7 @@ <h1 id="Make-a-Prediction">Make a Prediction<a class="anchor-link" href="#Make-a
1178511785
<div class="inner_cell">
1178611786
<div class="text_cell_render border-box-sizing rendered_html">
1178711787
<hr>
11788-
<p><strong>Rule 8: Expect Your Notebooks to be Read, Run, and Explored.</strong> We use ipywidgets to present to users a text box to execute a prediction for a protein sequence of their choice. We provide a default sequence to generate a reproducible result.</p>
11788+
<p><strong>Rule 9: Enable Your Notebooks to Be Read, Run, and Explored.</strong> We use ipywidgets to present to users a text box to execute a prediction for a protein sequence of their choice. We provide a default sequence to generate a reproducible result.</p>
1178911789
<hr>
1179011790

1179111791
</div>
@@ -11855,13 +11855,13 @@ <h2 id="Enter-a-Protein-Sequence-in-Text-Box">Enter a Protein Sequence in Text B
1185511855

1185611856

1185711857

11858-
<div id="e2a449a2-fb51-46d7-8b21-dc92befc4afb"></div>
11858+
<div id="b5407a67-474f-498e-bb1b-a5504d2f801b"></div>
1185911859
<div class="output_subarea output_widget_view ">
1186011860
<script type="text/javascript">
11861-
var element = $('#e2a449a2-fb51-46d7-8b21-dc92befc4afb');
11861+
var element = $('#b5407a67-474f-498e-bb1b-a5504d2f801b');
1186211862
</script>
1186311863
<script type="application/vnd.jupyter.widget-view+json">
11864-
{"model_id": "9bef296ce825422592439bdcd9ad4e96", "version_major": 2, "version_minor": 0}
11864+
{"model_id": "391ce7f51aca431387188610ba44d563", "version_major": 2, "version_minor": 0}
1186511865
</script>
1186611866
</div>
1186711867

0 commit comments

Comments
 (0)