Preferences

General Preferences

In the General Preferences, it is possible to enter a valid email address, which will be used in the QBLAST and also in the InterProScan searches. Furthermore, the path to the OmicsBox workspace can be provided and all results such as BLAST, InterProScan, charts and OmicsBox projects will be saved here.

Figure 3: OmicsBox General preferences

Update

OmicsBox allows automatic software updates during the application startup. These updates contain improvements, new features or bug fixes. It is possible to choose if you want to be notified of new updates or if you want to install software updates automatically (recommended).

It is also possible to specify the update behaviour of installed Apps. We differentiate between "Featured'' and normal Apps. New "featured'' Apps can be installed and updated automatically. Normal, non-featured Apps have to be installed manually but can be updated automatically.

GO Version

For the Functional Analysis Module OmicsBox contains the Gene Ontology database and all the information necessary to perform the mapping step i.e. to be able to link the different protein IDs to the functional information of the Gene Ontology database (see Gene Ontology Mapping section).

Here one can select the GO version available on OmicsBox servers as well as the corresponding .obo file to be used in the mapping step.

Local OmicsBox database

Local OmicsBox database installation: If you are interested in installing your own OmicsBox database locally with the aim to not depend on the OmicsBox server, you can find a tutorial on the OmicsBox website in the download section including a step-by-step installation guide. Basically will need a MySql server, the latest GO database dump and some additional "mapping tables" (NCBI and PIR flat-files). By following several few steps this data is imported into your database.

Enzyme Code Data

In OmicsBox it is possible to provide a file with the corresponding Enzyme Codes.

Figure 4: Wizard to configure the OmicsBox update behaviour

Proxy Settings

If a proxy server or a firewall is used to access the internet here you can define the proxy settings. An HTTP or a Socks proxy can be configured. In this window, you can configure the proxy settings only for OmicsBox and this will overcome the system-wide settings. If the Use Direct Connection check box is selected, the application will try to connect directly to the internet skipping any system settings. To use your defined proxy settings select the HTTP or Socks Proxy check box and complete the required fields.

Custom CA Root Certificates

This option allows the import of custom CA root certificates to the OmicsBox trusted entities. It is located in the same Proxy setting page.

A certificate authority (CA) is an entity that issues digital certificates. A digital certificate certifies the ownership of a public key by the named subject of the certificate (Common Name or CN in a certificate). A CA acts as a trusted third-party and allows OmicsBox to rely on the packets received through the connection to OmicsCloud or other internet sites. The format of these certificates is specified by the X.509 standard.

In a normal configuration, a secure connection is established between the end client (OmicsBox) and the server (e.g.: OmicsCloud) and the packages travel encrypted between client and server. In some custom firewall configurations where all traffic going through the network is inspected by the firewall, a secure connection is established between the client application and the firewall, and another connection is established between the firewall and the servers. The firewall can act as a man-in-the-middle to inspect the packages and will re-encrypt them using its own certificate.

This may cause connection problems if OmicsBox does not recognize the certificate used in the firewall as a trusted entity. The IT department of the institution will know if a custom certificate is used and can provide you with the CA root of this certificate, or the certificate itself, to be added to OmicsBox. This is usually a .crt file that can be provided in the wizard page.

It can also be obtained from a regular web browser by opening a page that is known to be inspected by the firewall, for example the connection to the OmicsCloud https://cloud.biobam.com by clicking on the padlock next to the url address the certificate option shows the path to the certificate and the signing authority. On our servers, the CA root entity is either Amazon Root CA 1 or GlobalSign Root CA. Something else is an indicator of a custom CA Root certificate.

In Windows and Linux, the Root certificate can be saved from within the browser.

In MacOS, this needs to be searched in the keychain app and exported from there. Once this file is exported, it can be directly imported in OmicsBox Proxy preferences page.

Figure 5: Proxy settings dialog

Whitelist domains for a Firewall

OmicsBox relies on a hybrid structure, melding desktop and cloud computing via Amazon Web Services (AWS). This setup requires uninterrupted online access to execute tasks and retrieve data from various resources, including key sites like Gene Ontology.

Given the cloud-based nature of our services, OmicsBox interacts with API endpoints with dynamic IPs, necessitating certain network allowances for full functionality.

Your network's firewall should explicitly allow outbound traffic to the following host domains to ensure proper operation. The Core category will make OmicsBox work with our cloud infrastructure. The Optional category entries include domains for third-party public services and resources used in OmicsBox.

Domain

Category

Description

*.biobam.com

Core

BioBam Resources

*.amazonaws.com

Core

BioBam Backend Infrastructure at AWS

*.cloudfront.net

Core

BioBam Backend Infrastructure at AWS (CDN)

*.salesforce.com

Core

In-App BioBam Support Mail

blast.ncbi.nlm.nih.gov

Optional

NIH NCBI BLAST Public Service

*.ebi.ac.uk

Optional

EMBL-EBI Public InterProScan Service

*.ensembl.org

Optional

Ensembl BioMart Public Services

geneontology.org

ftp.geneontology.org

Optional

Gene Ontology Resources

This whitelisting is crucial for the software to communicate effectively with the necessary external resources. Permitting access to multiple subdomain levels (e.g., a.b.c.biobam.com) within the main domains is also important.

By configuring your firewall to recognize and authorize these domains, you help guarantee the smooth, uninterrupted operation of OmicsBox within your infrastructure.