|
16 | 16 | "1. learn what a data pipeline is\n", |
17 | 17 | "2. create our first simple data pipeline in DataJoint\n", |
18 | 18 | "3. insert some data into the pipeline\n", |
19 | | - "4. basic queries to flexible explore the data pipeline\n", |
| 19 | + "4. basic queries to flexibly explore the data pipeline\n", |
20 | 20 | "5. fetch the data from the pipeline\n", |
21 | 21 | "6. delete entries from tables" |
22 | 22 | ] |
|
80 | 80 | "metadata": {}, |
81 | 81 | "source": [ |
82 | 82 | "> * Your lab houses many mice, and each mouse is identified by a unique ID. You also want to keep track of information about each mouse such as their date of birth, and gender.\n", |
83 | | - "> * As a hard working neuroscientist, you perform experiments every day, sometimes working with more than one mouse in a day! However, on an any given day, a mouse undergoes at most one recording session.\n", |
| 83 | + "> * As a hard working neuroscientist, you perform experiments every day, sometimes working with more than one mouse in a day! However, on any given day, a mouse undergoes at most one recording session.\n", |
84 | 84 | "> * For each experimental session, you would like to record what mouse you worked with and when you performed the experiment. You would also like to keep track of other helpful information such as the experimental setup you worked on. \n", |
85 | 85 | "\n", |
86 | 86 | "> * In a session of electrophysiology\n", |
|
148 | 148 | "cell_type": "markdown", |
149 | 149 | "metadata": {}, |
150 | 150 | "source": [ |
151 | | - "In the current notebook, we will design the tables for mouse and experimental sessions, the rest of the pipeline will be designed in the subdirectory `electrophysioloy` and `calcium_imaging`" |
| 151 | + "In the current notebook, we will design the tables for mouse and experimental sessions, the rest of the pipeline will be designed in the subdirectory `electrophysiology` and `calcium_imaging`" |
152 | 152 | ] |
153 | 153 | }, |
154 | 154 | { |
|
555 | 555 | "source": [ |
556 | 556 | "Note that, to uniquely identify an experimental session (or simply a **session**), we need to know the mouse that the session was about. In other words, a session cannot existing without a corresponding mouse! \n", |
557 | 557 | "\n", |
558 | | - "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We would graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) dependeing on the one above (**mouse**)." |
| 558 | + "With **mouse** already represented as a table in our pipeline, we say that the session **depends on** the mouse! We could graphically represent this in an **entity relationship diagram (ERD)** by drawing the line between two tables, with the one below (**session**) dependeing on the one above (**mouse**)." |
559 | 559 | ] |
560 | 560 | }, |
561 | 561 | { |
|
590 | 590 | "cell_type": "markdown", |
591 | 591 | "metadata": {}, |
592 | 592 | "source": [ |
593 | | - "You can actually generate the entity relationship diagram (ERD) on the fly by calling `dj.ERD` with the schema object" |
| 593 | + "You can actually generate something similar to an entity relationship diagram (ERD) on the fly by calling `dj.Diagram` with the schema object. Many of the symbols and features are the same as the ERD standard." |
594 | 594 | ] |
595 | 595 | }, |
596 | 596 | { |
|
599 | 599 | "metadata": {}, |
600 | 600 | "outputs": [], |
601 | 601 | "source": [ |
602 | | - "dj.ERD(schema)" |
| 602 | + "dj.Diagram(schema)" |
603 | 603 | ] |
604 | 604 | }, |
605 | 605 | { |
|
746 | 746 | "cell_type": "markdown", |
747 | 747 | "metadata": {}, |
748 | 748 | "source": [ |
749 | | - "We will introduce three major types of queries used in DataJoint:\n", |
| 749 | + "We will introduce four major types of queries used in DataJoint:\n", |
750 | 750 | "* restriction (`&`) and negative restriction (`-`): filter data\n", |
751 | 751 | "* join (`*`): bring fields from different tables together\n", |
752 | 752 | "* projection (`.proj()`): focus on a subset of attributes\n", |
|
911 | 911 | "cell_type": "markdown", |
912 | 912 | "metadata": {}, |
913 | 913 | "source": [ |
914 | | - "Let's find all mouse that **is not male** AND **born after 2017-01-01**." |
| 914 | + "Let's find all mice that **are not male** AND **born after 2017-01-01**." |
915 | 915 | ] |
916 | 916 | }, |
917 | 917 | { |
|
983 | 983 | "cell_type": "markdown", |
984 | 984 | "metadata": {}, |
985 | 985 | "source": [ |
986 | | - "All mice that has a session" |
| 986 | + "All mice that have a session" |
987 | 987 | ] |
988 | 988 | }, |
989 | 989 | { |
|
1534 | 1534 | "\n", |
1535 | 1535 | "In the next session, we are going to extend our data pipeline with tables to represent **imported data** and define new tables to **compute and hold analysis results**.\n", |
1536 | 1536 | "\n", |
1537 | | - "We will use both ephys and calcium imaging as example pipelines. The notebooks reside in the directory " |
| 1537 | + "We will use both ephys and calcium imaging as example pipelines:\n", |
| 1538 | + "+ [02-electrophysiology](../02-Electrophysiology/02-Imported%20Tables%20-%20Interactive.ipynb)\n", |
| 1539 | + "+ [02-calcium imaging](../01-Calcium_Imaging/02-Imported%20Tables%20-%20Interactive.ipynb)" |
1538 | 1540 | ] |
| 1541 | + }, |
| 1542 | + { |
| 1543 | + "cell_type": "code", |
| 1544 | + "execution_count": null, |
| 1545 | + "metadata": {}, |
| 1546 | + "outputs": [], |
| 1547 | + "source": [] |
1539 | 1548 | } |
1540 | 1549 | ], |
1541 | 1550 | "metadata": { |
| 1551 | + "jupytext": { |
| 1552 | + "formats": "ipynb,py:light" |
| 1553 | + }, |
1542 | 1554 | "kernelspec": { |
1543 | | - "display_name": "Python 3", |
| 1555 | + "display_name": "workflow-array-ephys", |
1544 | 1556 | "language": "python", |
1545 | | - "name": "python3" |
| 1557 | + "name": "workflow-array-ephys" |
1546 | 1558 | }, |
1547 | 1559 | "language_info": { |
1548 | 1560 | "codemirror_mode": { |
|
1554 | 1566 | "name": "python", |
1555 | 1567 | "nbconvert_exporter": "python", |
1556 | 1568 | "pygments_lexer": "ipython3", |
1557 | | - "version": "3.7.3" |
| 1569 | + "version": "3.9.4" |
1558 | 1570 | } |
1559 | 1571 | }, |
1560 | 1572 | "nbformat": 4, |
|
0 commit comments