emBASE User FAQ

How do I get a login?

Send an email to girardot@embl.de indicating your embl username (this will be your login). You'll receive an email containing your password.

After login, directly go to your user page (Users > My account) and change the pwd to what you like (at the end of the page). You can use your preferred pwd as pwd are encrypted in DB.

How do I export data?

If you want to export your experiment in Tab2Mage format, please see How do I submit an experiment to ArrayExpress

1. go to Analyze section
2. select an experiment
3. select the Analysis steps tab
4. Locate the line holding the dataset you want to export e.g. after normalization and Julien Gagneur's limmatest plugin run.
5. Then click the icon that says "Export data" when you move your mouse over (the icon is a db symbol with a green arrow getting out)
6. You then have different export options, depending on the format you like, whether data should be merged by reporter...
7. If you pick a "Custom" format e.g. Custom BASEfile, you'll be at a page with lots of fields you can select. There is a logic on the presentation but it might be a little confusing at first:

• In the first block columns, you have listed the reporter annotations you can include
• In the second block Fields, you have all fields that refer to feature data from the hybs. You'll notice that some fields are prefixed with Raw or LIMS, or Extra or nothing. You can ignore LIMS things. Raw fields means that they are linked to raw data (as found in the .gpr files i.e. before any normalization or analysis). Extra fields are values computed by plugins and those fields named like JG_*** are values from Julien Gagneur plugins. Finally un-prefixed fields are related to the spot intensities at the experiment level you selected.

I don't see the search field at top of each BASE page, what to do?

You have to change the current 'auto_increment' value of the 'base.search' table.

- Open the PHP log file - You should see something like:

MySQL query failed: "INSERT INTO Search (`sortField`,`sortDesc`,`currentPage`) VALUES (' ', '0', '0')" : Duplicate entry '985' for key 1

- In this case You have to update the new 'auto_increment' value to 986 (current value + 1)

- The SQL statement to update the table is

ALTER TABLE `Search` PACK_KEYS =0 CHECKSUM =0 DELAY_KEY_WRITE =0 AUTO_INCREMENT =986

How do I submit an experiment to ArrayExpress?

Use the Tab2Mage export page accessible from your experiment's analysis tree. A user manual covering this topic is available at the emBASE documentation center

I have tons of hybridizations to load in emBASE, what can I do?

When you have many hybridizations to load, you should use the batch uploader, BASELoader, that we have develop to answer this problem. You can access the service at this address. In addition to online help, a user manual and howto's are also available at the emBASE documentation center

What are the microarray platforms supported by emBASE?

We currently support spotted arrays (i.e. 2 channels arrays), Affymetrix, CodeLink? and NimbleGen. We'll support Agilent very soon. emBASE is very flexible, if you need support for another platform, please contact Charles Girardot.

Can I export my experiment in MAGE-ML?

No.

Why don't you use BASE 2?

Well we still consider that BASE 2 lacks several key features to compete with the platform that we have today. But we plan to migrate at some point.

The microarray I used is not available in the batch uploader, what should I do?

Please contact us and we'll add it.

I'd like to annotate my reporters but there is no annotation column matching my need, what can I do?

Reporter annotations can be customized. Please contact us and we'll add it.

I want to create new sample origins but I can't find how to do this.

It means you don't have adequate privileges. Some sensitive part of emBASE are locked and can be managed only by few people. Sample origins is part of these as they are shared by everybody. To keep it organized we decided to restrict the number of people that can edit them. Please get in touch with us and once we made sure you know the management rules of sample origins, we'll grant you with adequate privileges.

How do I properly describe IPed samples used in ChIP-chip experiments?

The emBASE schema is quite restricted in term of modeling all steps performed from a sample down to the labeled extract. In fact, you can only have one sample, one extract and one labeled extract. In the case of ChIP-chip, the usual model would more something like: sample => IPed sample => extract => labeled extract.  Unfortunately, we can't model it this way in the current version, the best (and not too costy) solution we found is to group the two first steps into the sample item: when you create/edit a sample, there is a flag Is ChIP Sample that you can turn on to indicate that this sample has been IPed. In this case, you must also attach a ChIP Protocol.

Should I upload hybridization scans (i.e. pictures) in emBASE?

It is up to you. Although it is true that Affymetrix scans are huge and take lot of space. This is why we don't recommend to upload Affymetrix scans or scans which size is nearly 1 Go. In the case of tiff pictures from spotted arrays, we kept them until now..

What are the available analysis plugins in emBASE?

To have an up-to-date list, please log in emBASE and go the plugins page (in the Data Analysis section).

Can I write my own plugin and have it in emBASE?

of course! Please contact us.

GeneCore has performed my hybridizations, what protocols should I use?

We have created ready to use "Standard" protocols for labeling and hybridization. There are usually different ones depending on the platform and chip types : Affymetrix ExpressionArray, Affymetrix ExonArray, Affymetrix TilingArray etc...In case of doubt, please contact us.

How do I connect to the emBASE fileserver to upload my files?

Everybody who has an account for emBASE, also has a folder (named as the user name) on the emBASE fileserver. This folder can be reached:

• For Unix: If you have a machine where /g/base is automounted, you can access your personal folder by typing cd /g/base/base_users_data/. If not, please check the information on this page -
  • http://www.embl.de/staffonly/services/cng/fileservices.html
• For Mac:
  • In the Finder, Menu "Go", select "Connect to Server"
  • Type the address "smb://EMBL;username@fsbase/base" in the Server Address (e.g. smb://EMBL;sauer@fsbase/base )
  • Hit Connect
• For Windows:
  • In Windows Explorer (Win key + e) click on 'Tools -> Map Network Drive', and a window will pop up.
  • Type in the name of the folder to connect (\\fsbase\base)
  • Press connect and you will be prompted for an user name and password. Use you usual EMBL login information.
  • In the opened window, go to “base_user_data” and then the folder named like your user name.

What is the emBASE personal space?

This is a directory reserved for you on the emBASE file server. This directory exists only for registered emBASE users. It is named after your EMBL login (e.g. furlong) and it is located on the emBASE file server, in the directory named base_user_data. Please see this FAQ entry How do I connect to the emBASE fileserver to upload my files to learn how to access your personal space (just above!). The main things to know about this personal space are:

• your personal directory is safe : you are the only person who can go in your personal directory (of course emBASE administrators can go there)
• your personal directory is a temporary storage place:
  • this is NOT where emBASE keeps data for long term storage : this place is used to temporarily place your data files so emBASE can find them easily and copy them into its protected area
  • these personal directories are monitored and data used by emBASE will be automatically deleted after some time (without warnings). Don't use this place to store data not related to emBASE!

How do I specify biological and technical replicates in emBASE?

There is nothing that explicitly models replicates. It is normally achieved by objects relationships and annotations:

1. extracts and libraries are linked to the same sample when they are technical replicates
2. samples with identical annotations are biological replicates

In practice, it is a little different i.e people usually do not pay too much attention to fulfill the first aspect. Therefore replicates need to be somehow flagged within the system, in particular using the sample annotation system. As already mentioned, replicate samples must have the same annotations: this is used to automatically group samples into replicate groups. But since some annotations might have a different goal, it might be a good idea to annotate samples of the same group or condition (ie all biological and technical replicates) with a replicate group annotation. Then, all you need to know is which are tech and which are biol. reps (which you can normally disentangle if point 1 is fulfilled but assume point 1 is not fulfilled).

I use free text annotation called 'pairingKey' and 'conditionGrouping'. The conditionGrouping is used to group all replicates together (note that you don t really need it as replicates must already have all annotation the same but this makes it cleaner and overcome problems due to using sample annotations for weird purposes), then the pairingKey is here to put tech rep together. When I process data, I automatically group samples based on 'conditionGrouping' and further merge paired samples.

Let's take an example:

2 time points, each with 2 biol reps. Second time point also have 2 tech rep for each biol rep).

Sample	conditionGrouping	pairingKey
Twist_2-4h_biolrep1	twi_24h
Twist_2-4h_biolrep2	twi_24h
Twist_4-8h_biolrep1-1	twi_46h	techrep1
Twist_4-8h_biolrep1-2	twi_46h	techrep1
Twist_4-8h_biolrep2-1	twi_46h	techrep2
Twist_4-8h_biolrep2-2	twi_46h	techrep2

In theory, if the data would be entered correctly in emBASE (only one sample for the tech rep), you would not really need all this : samples with same annotations would be biol rep. And the example above would be:

Sample	conditionGrouping	objects in emBASE
Twist_2-4h_biolrep1	twi_24h	biological => one extract => one library
Twist_2-4h_biolrep2	twi_24h	biological => one extract => one library
Twist_4-8h_biolrep1	twi_46h	biological => Two extracts => Two libraries OR(depending at what step the tech rep is made) => One extract => Two libraries
Twist_4-8h_biolrep2	twi_46h	biological => Two extract => Two libraries OR(depending at what step the tech rep is made) => One extract => Two libraries

Overall, there is not a single option. You need which approach you like best.