MIAMExpress Batch Upload Tool Help
In this help page:
The MIAMExpress Batch Upload Tool (Batchloader) is designed to provide fast submission of microarray experiments to ArrayExpress at the EBI. The tool is a stand-alone java application that is downloaded to your local machine and is an addition to the web form version of MIAMExpress (it does not replace it completely).
The batch upload tool can be used to create and edit MIAMExpress experiment submissions. It cannot be used to create and edit array designs and protocols.
You must submit required protocols through the MIAMExpress web forms before starting the batch upload tool:
If the array design you used is not already in ArrayExpress you must submit it through the MIAMExpress web forms before starting the batch upload tool:
You will need a MIAMExpress login account to use the batch upload tool. If you do not already have one then register here:
There is general information about ArrayExpress submissions, accession number assignment and data privacy here:
Batchloader is for submitting experiments to ArrayExpress. It's a stand alone tool that will download a small file to your local machine. Login with your MIAMExpress password. Submit your protocols via the MIAMExpress web interface first - you'll then be able to select these in batchloader. Any field in red is mandatory. Checks will prompt you for required information on each tab. Click 'Save & Next' when first entering data on a tab. Once you've saved on a tab you can use the top of each tab to navigate through the experiment submission.
Experiment tab: Add the details of your experiment, click the Affymetrix click box if you used only Affymetrix arrays and have one-to-one sample hybridization relationships. Submitters of mixed single/double channel experiments do not select Affymetrix. Click 'Save & Next' to get to the next tab to add publication info. If you need to quit at any point click save and close the window.
Publication tab: Add publication details if you have them. Click 'Save & Next' to get to the next tab.
Sample tab: Click multiply to create as many rows as you need. Completing common values in the first row prior to this will save time. Values in the name column must be unique. Excel-like functions from the top left toolbar or right click allow you to fill down, autoincrement etc. Select a whole column to paste by clicking on the header row or copy from Excel and use 'paste from worksheet' to add these values. Click 'Save & Next' to get to the next tab. Affymetrix users will automatically be directed to the Hybridizations tab. Submitters of two-colour experiments go to the Extract Tab.
Extract tab: Click multiply to add as many rows as you need. You can copy your sample names into the extract name column by using the tab (go back to the sample tab and click on the column header and right click 'copy column'. Now go back to the extract tab and click the extract name column header and right click to paste) or you can paste from a worksheet. Link extracts to samples by double clicking on each cell individually or if the sample to extract relationships are one-to-one you can copy and paste the sample names in from the previous tab.
LabeledExtract tab: This has changed from previous versions of batchloader. You can now assign your labels directly to extracts, they don't need to be linked to a protocol first. Create the number of labeled extracts you need by clicking multiply, select a protocol and a label for each extract.
Hybridization tab (two-colour): Create the number of hybridizations by clicking multiply as before. Assign two LabeledExtracts to each hyb. The labels will pop up next to linked extracts to help you enter the data. You can't edit them, they are for information only. Select an Array design name. You must have submitted self-made arrays via MIAMExpress to see them in the drop down list. Commercial arrays are also listed here. Select hybridization, scanning and normalization protocols (if you have normalized data). Upload data files by selecting them one by one, or cut and paste a list of path and file names into the Raw data column. You are limited to one normalized data file per hybridization and an additional processed data file for the whole experiment submitted on the final tab. Data file help describing formats and limitations is available. Click 'Finish' to get to the final tab.
Hybridizations tab (Affymetrix): Link the samples to the each labeled extract by selecting a Labeling Protocol. The system assumes a one-to-one sample-hybridization relationship for Affymetrix and will create the same number of hybridizations as samples. If this is not the case (e.g. you did technical replicates) you can add more hybs by selecting a row and multiplying it. When adding additional rows to an Affymetrix submission double click on a cell in the LabeledExtract column to generate a list of all Labeled Extracts and chose one. Label is pre-selected for Affy users. Select an Array Design name from the drop down list, right click and 'fill down' to add it to all rows. Upload data files by selecting them one by one, or cut and paste a list of path and file names into the Raw data column. You are limited to one normalized data file per hybridization and an additional processed data file for the whole experiment submitted on the final tab. Data file help describing formats and limitations is available. Click 'Finish' to get to the final tab.
Complete Submission: Once you've uploaded all your data files and checks are completed you can upload a final file. For example, if you used RMA and have a merged file for all hybs upload it here by browsing for it then select 'Submit' to save it. Click 'Complete Submission' to end. A visualization of the experiment will appear. You will get an email and our tracking system alerts the curators that the data can be curated. We will contact you with an accession number if everything is OK and with questions if we need more information. Your data will be released on the date you selected (you'll be reminded about this and can change the release date if necessary).
JRE (Java Runtime Environment) 1.5 is the minimum. Batchloader requires a web connection throughout the submission process.
If for any reason you lose the connection, or network traffic is heavy batchloader may slow down or hang. When starting batchloader if the application fails to download completely kill the download, check your network connection and try again. If batchloader hangs check the network connection, close the application and restart it. We recommend that you save each tab when you make modifications especially for large submissions.
PC and Mac support
Batchloader supports both Macs and PCs. Much of the spreadsheet type functionality has been provided from 'right click' and from a toolbar for both Mac and PC users.
Click on 'Start MIAMExpress Batch Upload Tool' - from the 'Experiment submission' tab of MIAMExpress.
A new empty browser window will open, and the application will download to your machine. Batchloader has a valid security certificate and will not harm your local machine or data in any way. Once batchloader is downloaded it will start automatically and you can login and begin your experiment submission. You can quit and restart batchloader at any point during the submission, by saving and then closing the window.
You can navigate between tabs to view or edit them either by using the 'Save & Next' or 'Previous' buttons at the bottom right of the tab:
or click on active tabs at the top of the tab:
If you log back into a saved incomplete submission use the 'Save & Next' button to navigate through the tabs.
There is a help tab at the far right of the tool bar; this is linked to general help documentation:
There is a help icon On the bottom left corner of each tab linked to that tab's help documentation:
Each column in the Samples, Extracts, Labeled Extracts and Hybridizations tab describes what should be entered in that column, shown here for organism on the Sample tab:
The toolbar is activated on the Samples, Extract, Labeled Extracts and Hybridization tabs. Use the toolbar icons at the top of the tab, or activate it by right clicking anywhere on a cell. The toolbar allows you to:
Auto-increment values in name column - adds an integer to each name to make these unique:
Insert rows. Inserts a copied row above the selected row:
Delete row. Deletes the row(s) selected by clicking on the row numbers:
Copy row. Copies row contents selected by clicking on the row numbers to insert as above:
Paste row. Pastes contents of a selected row, activated only when row(s) have been copied:
Visualize produces a node-edge diagram of the experiment so far. To include the contents of the current tab, you must first save the tab.
Functions available from right click menu
Note: Mac users should use the toolbar instead when deleting rows.
'Copy Column Downward' and 'Paste Column Downward' are very useful if you wish to carry across the associated entities to the next tab. For example, you can copy the Extract Names column downward from the Extracts tab and then in the Labeled Extracts tab, you can paste this column downward in the Extract Names column especially if the order between your labeled extracts and extracts is consistent.
Login to batchloader
Use your MIAMExpress user name and password to login to batchloader and click the ‘Login’ button.
Select 'New' to create a new submission, or select an experiment name from the drop down list to continue an incomplete saved submission. You cannot see any completed submissions in this list, if you need to edit a completed submission email the and we will make your submission available for editing.
Note that you can select and edit an experiment submission via batchloader or via the MIAMExpress web user interface. DO NOT edit in both tools at once. Choose one or the other.
The experiment tab is where you enter general information about your experiment. The help icons provide information on each field. Red text indicates mandatory fields.
Enter details of your publication here, details can be incomplete if the paper is submitted or in press.
Enter details of your samples, one sample per row.
You must provide a species and values for the factors you selected on the experiment tab. For example, for a developmental study in mutant mice, where development and differentiation design, and genetic modification design were selected, the experimental factors are genotype and developmental stage. Protocols must be submitted before selecting them here. If you forgot to do this:
The toolbar and right click functions are on this tab.
There are four categories of sample information (mandatory fields are shown in red):
Checking is applied when you save the tab; the error messages will alert you to any problems. Note that columns in red must have values e.g.:
Affymetrix users will proceed to the Hybridizations tab to upload data, 2-colour submitters will proceed to the extracts tab.
Here you are creating links between extracts and their samples and providing a protocol for extraction (mandatory) and any pooling - use this only if pooling of samples happened before nucleic acid extraction. The toolbar and right click functions are active on this tab so you can apply one protocol to all extracts. Double click and select one or more samples per extract. Affymetrix users typically will not see this tab.
Click save and then visualize to see the sample/extract relationships. Especially useful when describing pooling.
Labeled extract tab
Create as many labeled extracts as you need and link these to extracts by double clicking on a cell, or pasting a list of extracts from the previous tab. For example if you have 10 samples, 10 extracts and you did dye swaps create 20 labeled extracts and attach Cy5/Cy3 to each extract. Select a protocol from the list. The labeled extracts will be available for selection on the next tab
The hybridization tab is where you link labeled extracts to array designs to create the hybridizations, upload data files and provide protocols for hybridization, scanning and data normalization.
For rapid data entry create one hybridization, select the protocols, array design and then replicate this for the total number of hybridizations needed:
Adding labeled extracts
Affymetrix users will have auto created hybridizations, one per sample. You can create more by selecting a row and replicating it.
Uploading data files
Click on the data file field for each hybridization. Use the window to select data files or cut and paste file names and paths into the column.
For MIAME compliance you must submit raw data and normalized/processed data. The normalized/processed data can be in the form of a per hybridization normalized or processed data file uploaded here, OR a summary file per experiment (Final Gene Expression Data Matrix) uploaded on the next tab. If you are not submitting per hyb normalized data on this page do not select a normalization protocol.
There is more information on supported scanning software, and data file formats here:
Once you have uploaded the data files, click 'Save' at the bottom of the tab. The data files will be uploaded to EBI. This can be slow as these data files can be large, so please be patient. Click 'Finish' to access the final tab.
Access this tab by clicking 'Finish' on the Hybridization tab. Upload your final normalized, transformed data and select a data transformation protocol. Instructions on how to format this final gene expression matrix can be found in the data file help:
On completion of a submission you will see a visualization of the experiment and then be returned to the login tab. If you have not uploaded any normalized data then you will be invited to add some. MIAME requires that normalized data is provided for your experiment. You can start another submission or end the session by closing the batchloader window.
Please see the MIAMExpress help page for details:
Any further questions, please see our FAQ.