YEAST EXAMPLE PRINT
PLEASE NOTE: There are a few CPU-time intensive processes in this
procedure. You should be sure your HTTP Timeout has been adjusted on
your server before you proceed. Please see the install README for more
details.
CREATE SUIDs
The first thing that we are going to do is create SUIDs for a set of
yeast sequences. This involves the following steps.
On the LAD server copy the file:
/lad/install/yeast_example_print/yeast_pre_suids.txt
to
/home/curator/ORA-OUT/
In a web browser go to the link on the main page that says:
"Sequence IDs (SUIDs) (by file)"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Change the file name at the bottom of the screen to:
/home/curator/ORA-OUT/yeast_pre_suids.txt
Press "Assign SUIDs".
RETRIEVE SUIDs into PLATE FILE
On the LAD server copy the file:
/lad/install/yeast_example_print/yeast_retrieve_suids_into_plate.txt
to
/home/curator/ORA-OUT
In a web browser go to the link on the main page that says:
"Get SUIDs for Name in Plate File"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Change the file name at the bottom of the screen to:
/home/curator/ORA-OUT/yeast_retrieve_suids_into_plate.txt
Press "Get SUIDs".
The following file will be created:
/home/curator/ORA-OUT/yeast_retrieve_suids_into_plate.txt.SUID.oral
You will notice that the SUIDs have been merged into this file for the
given sequence names.
ENTER PLATES
In a web browser go to the link on the main page that says:
"Enter Plates (by file)"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Change the file name to:
/home/curator/ORA-OUT/yeast_retrieve_suids_into_plate.txt.SUID.oral
Set "Plate Name Prefix" to:
SC
Select a "Project":
Yeast
Type a "Plate Source":
Somewhere
Leave the rest of the fields as their defaults.
Press "Enter Plates"
This process can be time intensive - please be patient.
PLEASE NOTE: This process is time intensive due to heavy constraints
that are utilized to protect the database from corruption. This
process will complete and the delay is very much worth the assurance
that your data will always be protected and valid.
SELECT PLATES
Now it is time to select the plates back from the database.
In a web browser go to the link on the main page that says:
"Select Plates"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Select "SC" from the middle column below that.
Change the file name to:
/home/curator/ORA-OUT/sc_plates.txt
Press "Select Plates"
ENTER PRINT
If the plates had been used out of sequence we would now edit this
generated file [/home/curator/ORA-OUT/sc_plates.txt].
We will not do this, however.
In a web browser go to the link on the main page that says:
"Enter Print and Spotlist"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Change the File Name to:
/home/curator/ORA-OUT/sc_plates.txt
Set the Print Name to:
SC1
Set the Tip Configuration to:
32 Tip
Number of Slides:
400
Columns per Sector:
24
Rows per Sector:
19
Column Spacing:
175
Row Spacing:
175
Description:
Some description.
I also selected "Rotate Plates".
Press "Enter Print".
This is also a time consuming process - please be patient.
PLEASE NOTE: This process is time intensive due to heavy constraints
that are utilized to protect the database from corruption. This
process will complete and the delay is very much worth the assurance
that your data will always be protected and valid.
LOAD AN EXPERIMENT
It is now time to load an experiment.
We have provided a sample GPR, GPS, and two TIFF files for this purpose.
On the LAD server, copy the files:
/lad/install/yeast_example_print/250*
to
/home/curator/incoming
In a web browser go to the link on the main page that says:
"Experiments and Results"
Select "Saccharomyces cerevisiae" from the organism drop-down.
Press "Enter Experiments into LAD"
On the next screen...
For LAD Print Name select:
SC1
Type "Test" for the Slide Name.
Select 250.gpr for the Data File Location.
Select 250.gps for the Grid File Location.
Select 250_ch1.tif for the Green Scan File Location.
Select 250_ch2.tif for the Red Scan File Location.
Type "Test" for the LAD Experiment Name.
Type "Test" for the LAD Experiment Description.
Select "Test" for the Category and Subcategory.
Type "Green" for the CH1 Description.
Type "Red" for the CH1 Description.
Now press "Load Experiment into LAD"
The experiment is loaded into the queue.
In order to process it, you will need to execute the following program
on the server:
/lad/www-data/cgi-bin/SMD/queue/LoadExpt2DB.pl
oral
This program should be setup for CRON based operation. See the install
README file for more details.
NOTE:
There is a sample "batch" experiment file included in the
"/lad/install/yeast_example_print" directory. You may utilize it to see
an example of loading may experiments at once.
The file is --> "yeast_batch.txt".
Please refer to the batch submission of experiments in the online help
for more information.
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