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Commit 18e7d36e authored by Alice Dufour's avatar Alice Dufour
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Tables in doc/admin/README.md are completed. Sparse info is lacking and is signaled by 'xxx'

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...@@ -228,7 +228,7 @@ They correspond to different types of stocks. Each type is stored in a specific ...@@ -228,7 +228,7 @@ They correspond to different types of stocks. Each type is stored in a specific
| Field name | Type | What you enter in this field | | Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- | | ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer | | Id | Integer | A unique integer |
| Name | Character string | Plasmid's name (free text). Must be unique | | Name | Character string | Oligo's name (free text). Must be unique |
| Sequence | Character string | The DNA sequence of the oligo, always **5-prime to 3-prime** ! | | Sequence | Character string | The DNA sequence of the oligo, always **5-prime to 3-prime** ! |
| Description | Character string | A description of the oligo (free text) | | Description | Character string | A description of the oligo (free text) |
| Author | Character string | The lab member who obtained the oligo. Dropdown selection made from the `name` field of the `users` table | | Author | Character string | The lab member who obtained the oligo. Dropdown selection made from the `name` field of the `users` table |
...@@ -252,32 +252,148 @@ Clicking the `CopySeq` button copies the full oligo sequence to your clipboard. ...@@ -252,32 +252,148 @@ Clicking the `CopySeq` button copies the full oligo sequence to your clipboard.
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Strains <a name="Strains"></a> ### Strains <a name="Strains"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Name | Character string | Strain's name (free text) |
| Species | Character string | Strain's species. Dropdown selection made from the `name` field of the `species` table. |
| Other names | Character string | Strain's other name. Optionnal |
| General background | Character string | Genetic background of the strain. Dropdown selection made from the `name` field of the `backgrounds` table. |
| Comments | Character string | A description of the strain (free text) |
| Mating type | Character string | Strain's mating type. Dropdown selection made from the `alleles` field of the `st_mats` table. |
| ade2 | Character string | Modifications at ade2 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_ade2s` table. |
| his3 | Character string | Modifications at his3 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_his3s` table. |
| leu2 | Character string | Modifications at leu2 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_leu2s` table. |
| met15 | Character string | Modifications at met15 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_met15s` table. |
| trp1 | Character string | Modifications at trp1 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_trp1s` table. |
| ura3 | Character string | Modifications at ura3 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_ura3s` table. |
| ho | Character string | Modifications at ho locus. Leave empty if none. Freetext |
| locus1 | Character string | Modifications at a locus not mentionned in other fields. Free text |
| locus2 | Character string | Modifications at a locus not mentionned in other fields. Free text |
| locus3 | Character string | Modifications at a locus not mentionned in other fields. Free text |
| locus4 | Character string | Modifications at a locus not mentionned in other fields. Free text |
| locus5 | Character string | Modifications at a locus not mentionned in other fields. Free text |
| Parental strain | Character string | The id of the strain from which this one was obtained. Free text |
| Obtained by | Character string | Method used to obtain the strain. Free text |
| Checkings | Character string | Checkings performed on this strain such as PCR, or microscopy |
| Extrachromosomal plasmid | Character string | Any plamid present in this strain |
| Cytoplasmic character | Character string | Modifications of cytoplasmic contents. Free text. |
| Reference | Character string | Litterature refenrence related to the strain |
| Author | Character string | Person authoring this strain. Dropdown selection made from the `name` field of the `users` table. |
| Relevant plasmids | Character string | Plasmids related to the design of the strain. Free text |
| Relevant oligos | Character string | Oligos related to the design of the strain. Free text |
| Files | Media files | Uploaded media files of any format that you want to be associated with the strain |
| Created at | Timestamp | Timestamp of the record in the database |
| Updated at | Timestamp | Timestamp of updates |
| Warning | Boolean | Option used to signal an issue with the strain |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Antibodies <a name="Antibodies"></a> ### Antibodies <a name="Antibodies"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Antigen | Character string | Antibody's antigen (free text) |
| Host | Character string | Host of the antibody. Dropdown selection made from the `name` field of the `hosts` table. |
| Supplier | Character string | The company or service who supplied the oligo. Dropdown selection made from the `name` field of the `suppliers` table |
| Type | Character string | Type of antibody. Dropdown selection made from the `name` field of the `xxx` table. |
| Productid | Character string | Supplier's reference of the antibody (free text) |
| Batchid | Character string | Production batch reference (free text) |
| Instock | Character string | Stock status of the antibody. Dropdown selection made from the `name` field of the `xxx` table. |
| Ordered By | Character string | Person who ordered this antibody. Dropdown selection made from the `name` field of the `users` table. |
| Comments | Character string | A description or comment about the antibody (free text) |
| Created At | Timestamp | Timestamp of the record in the database |
| Obtention Date | Timestamp | Date when the antibody was obtained |
| projects | Relationship | Links to projects related to this antibody. Dropdown selection made from the `name` field of the `projects` table |
| Files | Media files | Uploaded media files of any format that you want to be associated with the antibody. |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Cell lines <a name="Celllines"></a> ### Cell lines <a name="Celllines"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Name | Character string | Cell line's name (free text) |
| Celltype | Character string | Type of cells. Dropdown selection made from the `name` field of the `cell_types` table. |
| Description | Character string | A description or comments about the cell line (free text) |
| Origin | Character string | Source from which the cell line was obtained (free text) |
| Author | Character string | Person authoring this cell line. Dropdown selection made from the `name` field of the `users` table. |
| Files | Media files | Uploaded media files of any format that you want to be associated with the cell line. |
| Projects | Relationship | Links to projects related to this cell line. Dropdown selection made from the `name` field of the `projects` table |
| Created at | Timestamp | Timestamp of the record in the database |
| Updated at | Timestamp | Timestamp of updates |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Notebooks <a name="Notebooks"></a> ### Notebooks <a name="Notebooks"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Serial number | Character string | Reference number of the notebook. (free text) |
| Author | Character string | Author of the notebook. Dropdown selection made from the `name` field of the `users` table. |
| Begin Date | Date | Date at which the notebook was started |
| End Date | Date | Date at which the notebook was ended |
| Created at | Timestamp | Timestamp of the record in the database |
| Updated at | Timestamp | Timestamp of updates |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Pipets <a name="Pipets"></a> ### Pipets <a name="Pipets"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Serial number | Character string | Reference number of the pipet. (free text) |
| Brand | Character string | Pipet's brand. Dropdown selection made from the `name` field of the `suppliers` table. |
| Type | Character string | Pipet's type such as volume of number of channels. Dropdown selection made from the `name` field of the `pipet_types` table. |
| Files | Media Files | Uploaded media files of any format that you want to be associated with the pipet. |
| History | Character string | xxx |
| Created at | Timestamp | Timestamp of the record in the database |
| Updated at | Timestamp | Timestamp of updates |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Well plates <a name="Wellplates"></a> ### Well plates <a name="Wellplates"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Format | Character string | Plate's format (free text) |
| Name | Character string | Plate's name (free text) |
| Author | Character string | Person authoring this wellplate. Dropdown selection made from the `name` field of the `users` table. |
| Content Type | Character string | Plate's content (free text) |
| Thawings | Integer | Number of times the plate was thawed |
| Freeze Date | Date | Date at which the plate was frozen |
| Files | Media Files | Uploaded media files of any format that you want to be associated with the plate. |
| Freezer Id | Integer | Freezer in which the plate is kept |
| Comments | Character string | Comments or description about the weelplate (free text) |
| Warning | Boolean | Option used to signal an issue with the plate |
| Created at | Timestamp | Timestamp of the record in the database |
| Updated at | Timestamp | Timestamp of updates |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
...@@ -328,7 +444,7 @@ They correspond to pieces of information that are linked to stocks. Each type of ...@@ -328,7 +444,7 @@ They correspond to pieces of information that are linked to stocks. Each type of
| Name | Character string | Feature's name (free text) | | Name | Character string | Feature's name (free text) |
| Comments | Character string | Free text giving comments on the feature | | Comments | Character string | Free text giving comments on the feature |
| Created At | Timestamp | Timestamp of the record creation in the database | | Created At | Timestamp | Timestamp of the record creation in the database |
| Created At | Timestamp | Timestamp of the record update in the database | | Updated At | Timestamp | Timestamp of the record update in the database |
| Color | Character string | The color with which the feature will be displayed on plasmid maps. Do **NOT** edit directly because your color name or syntax may not be recognized properly. Instead, select one of those proposed by the dropdown menu | | Color | Character string | The color with which the feature will be displayed on plasmid maps. Do **NOT** edit directly because your color name or syntax may not be recognized properly. Instead, select one of those proposed by the dropdown menu |
After adding or editing DNA features entries, your **modifications will NOT directly appear on the plasmid maps** unless you intentionally **update plasmid maps with the latest features**. Technically, this corresponds to updating the BLAST database containing the DNA features sequences. To achieve this update, go to the `browse` page of the `DNA features` and click on the blue button (top right) labeled `Update Plasmid Maps with these Features`. After adding or editing DNA features entries, your **modifications will NOT directly appear on the plasmid maps** unless you intentionally **update plasmid maps with the latest features**. Technically, this corresponds to updating the BLAST database containing the DNA features sequences. To achieve this update, go to the `browse` page of the `DNA features` and click on the blue button (top right) labeled `Update Plasmid Maps with these Features`.
...@@ -339,25 +455,58 @@ Now your latest changes should appear on the [plasmid maps](#Plasmidmaps). ...@@ -339,25 +455,58 @@ Now your latest changes should appear on the [plasmid maps](#Plasmidmaps).
### Events <a name="Events"></a> ### Events <a name="Events"></a>
xxx
| Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Datatype | Character string | Type of data |
| Event date | Date | Date of the event |
| Event type | Character string | Type of event |
| Description | Character string | A description of the event. (free text) |
| Files | Media | Any media you may want to upload regarding the event |
| Created At | Timestamp | Timestamp of the record creation in the database |
| Updated At | Timestamp | Timestamp of the record update in the database |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Passages <a name="Passages"></a> ### Passages <a name="Passages"></a>
xxx | Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Cell line | Character string | The cell line this passage is about |
| Name | Character string | Passage's name (free text) |
| Author | Character string | Author of the passage. Dropdown selection made from the `name` field of the `users` table. |
| Freezing Date | Timestamp | Date when the passage was frozen |
| Created At | Timestamp | Timestamp of the record creation in the database |
| Updated At | Timestamp | Timestamp of the record update in the database |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Species <a name="Species"></a> ### Species <a name="Species"></a>
xxx | Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Name | Character string | Specie's name (free text). Must be unique, will appear in dropdown selections. |
| Created At | Timestamp | Timestamp of the record creation in the database |
| Updated At | Timestamp | Timestamp of the record update in the database |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Suppliers <a name="Suppliers"></a> ### Suppliers <a name="Suppliers"></a>
xxx | Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Name | Character string | Supplier's name (free text). Must be unique, will appear in dropdown selections. |
| Created At | Timestamp | Timestamp of the record creation in the database |
| Updated At | Timestamp | Timestamp of the record update in the database |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
### Storage locations <a name="Storage"></a> ### Storage locations <a name="Storage"></a>
...@@ -418,7 +567,17 @@ For your information, boxpositions are referenced by the id of the box, and by t ...@@ -418,7 +567,17 @@ For your information, boxpositions are referenced by the id of the box, and by t
### Projects <a name="Projects"></a> ### Projects <a name="Projects"></a>
xxx | Field name | Type | What you enter in this field |
| ---------- | ---- | ---------------------------- |
| Id | Integer | A unique integer |
| Name | Character string | Project's name (free text). Must be unique, will appear in dropdown selections. |
| Leader | Character string | Leader of the project. Dropdown selection made from the `name` field of the `users` table. |
| Files | Media | Any media you may want to upload regarding the event |
| Status | Character string | Project's status. |
| Description | Character string | A description of the project. (free text) |
| Created At | Timestamp | Timestamp of the record creation in the database |
| Updated At | Timestamp | Timestamp of the record update in the database |
*[Back to Contents](#Contents)* *[Back to Contents](#Contents)*
......
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