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# Building CoNekt | |
## Using the admin panel to build CoNekt | |
Make sure *LOGIN_ENABLED=True* in *config.py* and the database was build | |
with and admin account. Next, go to the website, log in and (once logged | |
in) click on the username (admin) in the top right corner. Select 'Admin | |
Panel' from the drop-down menu. | |
![Admin panel](./images/admin_home.png "admin panel") | |
The Admin Panel will welcome you with a large warning. Deleting data, | |
overwriting or changing entries here can ruin a carefully set up | |
database. Make sure to read instructions on pages and this documentation | |
to avoid losing work. When working with an existing database, make sure | |
to back up the database before proceeding. | |
### Adding GO terms and InterPro domains | |
Descriptions for GO terms and InterPro domains should be added before | |
adding functional annotation. This step should be completed first. In | |
the top menu click on 'Add' and select 'Functional Data'. | |
![Add functional data](./images/add_functional_data.png "Adding functional data") | |
The GO descriptions can be obtained from the Gene Ontology Consortium's | |
official website in OBO format [here](http://geneontology.org/page/download-ontology). | |
InterPro domains and descriptions (called the **Entry list**) are found on EBI InterPro's download pages [here](https://www.ebi.ac.uk/interpro/download.html), | |
decompress the .gz file prior to uploading. | |
Click the buttons on the page and select the corresponding files, next | |
click 'Add functional data' to upload the files to your server and | |
import them in the database. This process can take some time, do not | |
close the browser window. | |
**Note: The existing tables will be cleared before adding the new | |
definitions. Do not update this information if GO/InterPro data is | |
already added to species !** | |
### Adding a new species and functional data | |
Adding a species requires multiple steps, follow the steps below for | |
each species. | |
#### Adding the species and sequences | |
On the 'Admin panel', under 'Add' select 'Species'. Fill in the | |
full scientific name (or the name you wish to appear on the website) for | |
the species and select a 'three letter code', that is unque for the | |
species (we recommend a combination of genus and species cfr. **H**omo | |
**sa**piens = hsa, note that while three characters is recommended it is | |
not required, longer codes are possible). | |
Some visualizations require a color specific for each species, these can | |
be entered using the controls below (clicking the box opens a color | |
picker, there is no need to manually add in hex values). | |
Finally, select a fasta file with **coding sequences**, in the fasta | |
headers the gene name (and only the name) needs to be present. These are | |
the names genes will receive on the website. | |
``` | |
>Gene1 | |
ATG... | |
>Gene2 | |
ATG... | |
``` | |
To upload the data and add the species to the database click 'Add species' | |
#### Adding functional Annotation to sequences | |
**GO** terms can be imported from tab delimited files, containing 3 | |
columns: gene name, GO label and the evidence tag. | |
``` | |
Gene1 GO:0004621 IEA | |
Gene1 GO:0004622 IEA | |
Gene2 GO:0000227 ISS | |
... | |
``` | |
On the 'Admin panel', under 'Add' -> 'GO Genes' such a file can be | |
uploaded, for a species. Additionally a description needs to be provided | |
from where the GO terms in the file originate from (the source). | |
![GO gene](./images/add_go_gene.png "Adding GO terms for a species") | |
**InterPro** domains can be imported directly from [InterProScan](http://www.ebi.ac.uk/interpro/download.html) output. | |
To do so, in the 'Admin panel', under 'Add' -> 'InterPro genes' select a species, select the file and click 'Add InterPro' | |
![InterPro gene](./images/add_interpro_gene.png "Adding InterPro terms for a species") | |
### Adding expression data | |
Expression data should be processed using [LSTrAP](https://github.molgen.mpg.de/proost/LSTrAP), | |
this will generate the expression matrix, coexpression networks and | |
clusters that can be directly imported into CoNekt. Note that in | |
some cases additional files, containing meta information, need to be | |
provided. | |
#### Adding expression profiles | |
In the 'Admin panel', under 'Add' -> 'Expression profiles'. Select the | |
species and the source (currently only LSTrAP expression matrices are supported). | |
Next, select the expression matrix (generated using LSTrAP). Using a | |
normalized (TPM or RPKM) matrix is strongly recommended ! | |
Furthermore two additional files need to be provided, one that links the | |
run identifiers to specific conditions. This tab delimited file should | |
be structured as indicated below, a one-line header (which is ignored) | |
and two columns, the first with the sample ID and the second with a short | |
description of the condition sampled. Samples with the same description | |
will be treated as replicates ! Omitting the condition description will | |
exclude the sample from the profiles. | |
``` | |
SampleID ConditionDescription | |
SRR068987 Endosperm | |
SRR314813 Seedlings, 11 DAG | |
SRR314814 | |
SRR314815 Flowers (floral buds) | |
SRR314816 | |
... | |
``` | |
For profile plots on the website most likely a custum order of conditions | |
is preferred. (We usually order tissues from bottom to top) A file to | |
specify this needs to be provided, conditions need to be stated in the | |
orther they should appear in the plot. | |
Furthermore a color for that condition in the plot needs to be added in | |
rgba() format. See the example below. | |
``` | |
Roots (apex), 7 DAG rgba(153, 51, 0, 0.5) | |
Roots (differentation zone), 4 DAP rgba(153, 51, 0, 0.5) | |
Roots (elongation zone), 4 DAP rgba(153, 51, 0, 0.5) | |
Roots (meristematic zone), 4 DAP rgba(153, 51, 0, 0.5) | |
Roots (QC cells), 6 DAS rgba(153, 51, 0, 0.5) | |
Roots (stele cells), 7 DAS rgba(153, 51, 0, 0.5) | |
Roots (tip) rgba(153, 51, 0, 0.5) | |
Leaves (rosette), 21 DAG rgba(0, 153, 51, 0.5) | |
Leaves (rosette), 29 DAG rgba(0, 153, 51, 0.5) | |
... | |
``` | |
If all files are selected click 'Add Expression Profiles' to upload the | |
data and add everything to the database. | |
![Add expression profiles](./images/add_expression_profiles.png) | |
#### Adding coexpression network | |
*UNDER CONSTRUCTION* | |
#### Adding coexpression clusters | |
*UNDER CONSTRUCTION* | |
### Adding external references | |
*UNDER CONSTRUCTION* | |
### Computing enrichments, similarities, and counts ... | |
*UNDER CONSTRUCTION* |