Fall 2001 to current time...

2000-2001 Academic Year

Submitting GCAT Datasets to SMD (Stanford Microarray Database)
Remember we are their grateful guests!

Whenever microarrays are printed, there must be a master file that identifies each spot. SMD has called this file a "godlist" and the godlist for our chips from Pat and Barbara is called yO1 which stands for Yeast Open reading frame #1.

Note that you can have more than 1 slide in a batch file; you just add it as another row (just need one header row at the top). Also, you might want to have a uniform convention for caps or lowercase for the file extensions (.tif vs .TIF) and be sure to keep the same case in the batch file as in the actual file.

Firstly, for your sample batch
There are sample Batch Files in Excel available for GCAT users.

When you are done, you should save it as a tab delimited text file before sending it to Barbara. You may submit multiple experiments with the same batch file. Just use a new row in the excel spreadsheet for each experiment.

While in Excel, if you set the format of the Expt Date field to "text", you can get it to display 2000-12-25.

Secondly, you should let people know that the "SMD Experiment Name" must be unique in the whole SMD database, so they should never have the same name (if it's an experiment redo, you'd have to name it "ExptRedo" or "Expt2" or something). Also, I've noticed that people are calling the green and red tif files something like yO1n112Cy3.TIF ...this is fine and it might even be an easier nomenclature. Just make sure that they match the names in the batch file (the people doing it this way have made sure the names match, so that's good).

Also, for the Experiment description, people might want to put the name of the students who did the expt, or refer to the lab notebook page that describes the hybridization, etc.... you can really use this field to keep detailed track of the experiment. A lot of the time it's just a repeat of the Experiment name, which seems a bit of a waste! Also, people aren't putting in their college and/or class and/or student names, and I'm sure they want them to appear somewhere! Of course, Malcolm can rename the files later to include this if you don't when submitting the files.

Academic Years Since Fall 2001

Accessing your tiff files

I have set up an FTP site at The Institute for Systems Biology (ISB) that will allow us to exchange data files. You cannot access these files with a web browser, you must use an FTP program.

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© Copyright 2001 Department of Biology, Davidson College, Davidson, NC 28036
Send comments, questions, and suggestions to: macampbell@davidson.edu