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User Guide

Artemis is a genome viewer developped by the Sanger Institute that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis has been modified to access Agmial servers and to display features like MuGeN (Box coloration, Features shapes).
This page only describes the modifications made to the standard version of artemis. For a complete user guide of artemis, see Sanger site.

System Requirements

Artemis will run on any machine that has a recent version of Java.

Agmial access

Artemis Launch

Link to artemis
First, click on the artemis link. This will lauch Java WebStart that will try to download and install the application.
(Nothing happens ? See Faq). If needed, select javaws (JNLPFile under Windows) as the default program to open jnlp files. ( See FAQ)

Artemis Loading

Java and Artemis Loading
First Java Webstart is loaded and check you version of Java [1]
Then, the application is loaded (or updated) from our servers [2].

Security Constraints

Security Constraints
Due to security constraints, the application need your agreement to access to local files. Accept it by clicking on OK[1].

Inra Agmial Access

Inra Agmial Access
Artemis has been extended to acces agmial data. To do so, juste choose the item "Inra Agmial Access" (shortcut : ctrl+A)[1].


Artemis Authentification
Then, enter your Agmial password and login in the appropriate fields.

Agmial Project Dialog

Choose the project [1], batch number [2], contig [3] and position [4] that you wish to display.
Then click on "Browse"[5].


artemis view of the genome
Artemis the load the protion of the genome you selected.
You are now able to navigate through the genome. A click on a CDS feature open its PAM page (resuming results and annotations) in the default web browser (Not the right one ? See FAQ)



Question: When I click on the artemis link, nothing happens

First of all, verify at this address that you have a valid Java software installation. You should - at least - have Java 1.4.2 . If not, follow the instructions on thoses pages to install it.

Question: When I click on the artemis link, my browser ask me what I want to do with the file.

You have to associate the type of files Java WebStart use to define deployable applications (JNLP file) with the appropriate programm (javaws for Linux, JNLPFiles for Windows).

Open With Dialog Box
Under Firefox, the browser asks you "What should Firefox do with this file ?". Clik on browse [1] and navigate to the javaws executable. Select it[2] and click ok.

Open With Dialog Box
You have now the Java Webstart application defined to open that file [1]
. By clicking on the "Always perform this action for that kind of file" checkbox [2], you save you preferences.

Question: When I click on a feature (with Agmial Protein Browsing enabled), artemis launches Internet Explorer© instead of my prefered browser (Firefox, for example)

Artemis is set to lauch your default browser. How to change your default browser