Frequently Asked Questions

How do I access the EADHB Database?
What can I do with the EADHB Database?
What kind of information is stored in the Local Database/Central Database?
Can I submit data without having access to the Web?

Problems and Technical Information:

How do I download and install the software?
How can I tell if my computer already has Java installed and what version?
What version of Java do I need to have installed?
Why do I have problems submitting to the Central Server/Launching the Database/downloading the software?

How do I access the EADHB Database?

The EADHB Gene Expression Database is accessed by a Java interface. The program will allow the user to input new expression data entries as well as to search the existing Central Database.

Java 1.4.2 should be installed (Java WebStart is included in this package). The database can then be downloaded and once installed can be run independently of internet access. You can access the links to these programs on the Downloads page.

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What can I do with the EADHB Database?

The EADHB database is a single package which allows the user to both enter data and perform searches. You are free to create your own local databases, unique entries of gene expression data, upload entries to the central database to contribute to the information resource and of course to search the central database for entries that may be of interest to you.

• Create and manage a local database. The user can create a database on their own computer which is linked to the central database only in accessing information about the anatomical tree structure and 3D standardised models. This database is not visible to any other EADHB database user, including the editors of the central database. The user can use the local, confidential copy of the database to store their own records and experimental data for easy access and searching with the knowledge that it is not viewable by anyone else.
• Enter expression data to unique entries within the database. The database allows the input of gene expression data (by mapping through a program called MAPaint - available upon request). The gene and specimen details, experiment information and original data pictures can all be included in this entry. In addition to the data entered by the user, the database software will automatically find the equivalent section related to the mapped data in the standardised 3D model and include an image of this section with the mapped data shown in various colours related to the signal strength.
• Upload information to the Central Database. The main aim of the database is to have as many people uploading results to the central database as possible to increase the usefulness of the database as an information resource. It is hoped that any groups creating relevant data will not only create entries in their local database but will also upload their finished entries to the Central Database for others to view and search. It is understood that there is a need for some confidentiality for unpublished results but once the results have been published the Central Database can be updated with any new entries quickly and easily.
  *NOTE: The data is uploaded to the Central Database but is not made visible immediately. Each new entry is looked at by the database editorial team before being made public, ensuring that there is time for users to contact the EADHB group and that all entries are checked for quality control.
• Searching the Central Database. The most important part of the database on a functional level is the ability to search the Central Database for gene expression results. As detailed in the About the EADHB Database pages, there are a number of ways to search the database ranging from text searches for a particular gene to see where it is expressed through to searching a particular anatomical region for any genes that are expressed there. The EADHB database also allows the user to search the EMAGE mouse gene expression database concurrently with the EADHB database to aid in Mouse v Human comparisons.

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What kind of information is stored in the Local Database/Central Database?

A database entry will contain several pieces of information required by users performing searches and wishing to gain knowledge from the entry. Data about the experimental user (e.g. person submitting, Principal Invesigator, Research Institute, contact details), probe being used (e.g. template DNA, probe name, accession ID, probe type) and specimen details (e.g. Carnegie Stage number, specimen preparation and sectioning details, images of original specimen and experimental data) are all included in the entry tables. A page for expression mapping data is also available. This includes the mapped data itself placed onto a specific section from the standardised 3D model showing strong, moderate, weak and undetected expression. An image of the original expression data (section or wholemount image) is also included as is a 3D representation of where the expression appears within the standardised model. The anatomical ontology tree is also included and if relevant links are present will also show which structures the expression is occuring in.

Although the data held in a local database is stored in the same format as that of the central database, there is much more information available in the central database due to many users inputting information. The local database is also secure and not visible to the rest of the world whereas the central database is visible to anyone who is willing to register to download the software.

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Can I submit data without having access to the Web?

Although the easiest and quickest way to submit entries from a local database to the central database is by using the internet and the interface within the database itself, it is still possible to submit data even if you can not get access to the internet on the computer you are using. There are a number of options open to the user.

Experimental data, be it section or wholemount data, can be captured with a digital camera and saved as a colour image. This image can then be sent to us at the address on the contacts page. We will then map the data to the model and add the expression patterns to the database. You must ensure that any information required by the database is included with the images sent. This includes:

• Name and contact details of at least one submitting author.
• Name and contact details of the principal investigator of the group.
• The name of the probe used in the experiment.
• The name of the gene along with the symbol and accession numbers when known.
• The carnegie stage of the specimen being used.
• [Remeber that the more information you include the more complete the entry will be and the easier it will be to chase up old experimental data]

Provided that the data are not too large the image and relevant information can be e-mailed to us at eadhb@ncl.ac.uk

The other option available to users who already have their own local database is to copy all the information onto a CD and then send it to the address on the contacts page. The directory where the database is located on the local machine will contain a series of directories. Each of these directories are a single entry into the database and contain the database entry, the original image file and any 3D movies, mapped data and other sample images the user may have added to the database entry. The entire directory of interest should be compressed (zip is a standard format used) and sent to us via e-mail if small enough or via CD if more than one entry is being sent.

The above steps will allow the EADHB group to be able to add the data to the database and upload the results into the Crentral Database server for public viewing.

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How do I download and install the software?

The Download pages contain the links to the various software. You need to download the installation file for Java 1.4.2 (which contains Java WebStart). Once this has been downloaded and installed you can click on the link to the database and you will be given an option to save the file or to start/run the program. It is recommended to save the file and then start the database software by double clicking on the saved file to start the database. This will install the software and enable you to access your local database without having to access the web-link each time.

If there is any doubt in the installation process or you think there may be security issues about installing new software then please ask your systems administrator for advice.

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How can I tell if my computer already has Java installed and what version?

You should ask your systems administrator for help if you ae unsure as to whether Java is installed on your computer. They will also be able to advise you on which version is installed.

The database is designed to work with the latest version of Java and more recent operating systems. To find out what version of Java is installed simply type the following command into a command prompt/terminal window: "java -version". You will be given details on the Java version that is currently installed. If Java is not installed this will not work so it will need to be installed.

Alternatively, if you access the Java web-site download page it will automatically detect the settings and install the latest version of Java if you do not already have it.

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What version of Java do I need to have installed?

It is recommended to have the latest version of Java installed (Java 1.4.2) together with the latest version of Java WebStart (this is included with the Java download). The database will work with Java 1.4.1 but if your machine does not have this installed then you will need to install the latest version as this version has been removed from the Sun/Java web-site.

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Why do I have problems submitting to the Central Server/Launching the Database/downloading the software?

The user may experience problems connecting to the Central Database and launching the software required to run the database in some circumstances. Usually this will involve a problem with a firewall set up on the users end. To overcome this we will need to know specific details of the firewall setup but it is a good idea to contact your system administrator or firewall administrator and find out if there is anything they can do.

Occasionally the EADHB central database may be offline for maintenance purposes. This should not stay this way for too long and so connecting again the next day is recommended.

Problems launching the database may be due to the incorrect version of Java WebStart being installed (or not being installed at all). If this is the case then it is simply a matter of following the instructions on the Downloads Page and installing the correct version and trying again. Another reason for this failing would be due to trying to run the software from the remote server when it is down for mainteneance. Wait and try again in a day or two.

If there are problems downloading the software then it may be possible that the server is down and you cannot connect to access the links. Otherwise check to make sure you have permissions to save the files being downloaded and that there is enough space left where you are attempting to save the files.

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