Submission process consists of uploading a data file and uploading metadata. There are 2 major ways of submitting the parameters (metadata): filling in the webform and pointing to a datafile (for a specific assay or experiment) or uploading a single parameter file (for many assays or experiments) along with the data (avoiding the webforms). The second option is called batch upload, because it allows a user to upload data for many assays/experiments in one go and at the same time to submit the annotation in a tab delimited format (rather than filling in the webform).

To submit individual files follow the steps:

Let's assume that you have a single file with results for an assay or experiment

1. log into the AIMS
2. choose your technology
3. go to "Assays" or "Experiments" page (click one of the tabs on the top side of the screen)
4. choose an assay or experiment from the list
5. click "Edit" button at the end of the row with this record
6. Once you are on "Edit" page, scroll down and point to the result file in the corresponding field, click "upload"

To submit data in batch:

I. Prepare the data:
Data files for a submitted group of assays/experiments can be either zipped in a single folder or put in a directory structure and then zipped. Once the zip folder with the results is ready (i.e. you have it ready on a local machine or have it uploaded to ftp), you have to prepare a parameter file - file containing the names of all data files and details of all assays/experiments.

II. Prepare the metadata:

Each row of this metadata file ("parameter file") contains names of a result file ( as in a zip folder) or a path within a folder.
For example, if a zip folder named "a.zip" contains:

- data1.txt
- subdir/data2.txt
- subdir/subdir2/data1.txt

Parameter file should refer to data files as "data1.txt", "subdir/data2.txt", "subdir/subdir2/data1.txt".

This will provide the necessary link between experiment annotation and the data itself.
The metadata file also can provide a third level id from SIMS (to joint AIMS and SIMS data), and all other parameters which a user might want to submit.

The easiest way to build a parameter file is to generate and excel file, using the header template,
which can be downloaded from the AIMS. The header is technology-dependent, so you'll have to:

1. log into the AIMS
2. select your technology
3. go to the section "Assays" or "Experiments" (click one of the tabs on the top side of the screen)
4. choose the tab "Upload Assays" or "Upload Experiments" in the top side of the screen
5. the page you'll see will contain a link to the template for this technology named "Download technology header".

III. Submission:
Once you have the data and metadata ready, perform the following steps:
1. log into the AIMS
2. select your technology
3. go to the section "Assays" or "Experiments" (click one of the tabs on the top side of the screen)
4. choose the tab "Upload Assays" or "Upload Experiments" in the top side of the screen
5. Point the system to the parameter file on your machine, using the "Browse" function
6. Point the system to the data file (either on the local machine, or in a zip folder on ftp), using the drop-down menu
7. Click "Upload"