- Recent files: Allows reopening recently closed projects.
- Open file: Open an OmicsBox project (.b2g/.box).
- Save and Save as…: Save the current project.
- Load: Allows loading of different file types into OmicsBox.
- Export: Allows exporting the desired information to some file types, such as text or GFF.
- Manage License: Check the license you currently have and change the activation key.
- Preferences: Set the OmicsBox configuration.
Data Import and Export
Under the File menu and the Tools sub-menu, there are several useful features that can be used to manipulate sequence data.
- Extract and import sequences from a FASTA and a GFF/GTF file (figure 1). For further information, please link here.
- Load Blast and InterProScan results.
- Load ID lists.
- Load GTF/GFF2/GFF3
- Load Accession List: Load Gene Ontology annotations via an Accession list.
- Load GeneSymbol List: Load Gene Ontology annotations via a GeneSymbol list.
- Load GI-List: load Gene Ontology annotations via a GenInfo Identifier (gi) list. Please consider the identifier to be between vertical bar e.g. gi|356569257|.
- Load Data from BioMart: Load Gene Ontology annotations from BioMart. For further details on how to load annotations, link here.
- Load EggNOG, Metagenomics and PfamScan annotations.
- Load metagenomic Kraken data.
- Load Count Tables and Differential Expression results.
- Load BAM and VCF files.
The Accession List and the GeneSymbol file should contain two columns (separated by tabs) per line. The first column the accession id or gene symbol and the second column may contain the corresponding taxonomy. The second column is optional.
Figure 1: Extract and import sequences from a FASTA and a GFF/GTF file.
- Generic Export: This option allows you to export all the desired information to a text file.
- Export Selected Sequences as Project: Only the selected sequences can be exported and saved in .dat file.
- Export Sequence Table: Export the current Main Sequence Table for the selected sequences.
- Export TopBlast data: It will export the best-blast-hit for each sequence, this is the hit with the lowest e-value.
- Export GO Propagation: Exports the GO parents up to the root for the annotated sequences.
- Export Sequences per GO (Gene Set).
- Export GFF: This option is only visible if a GFF file is loaded in OmicsBox or if a GFF has been generated from Gene Finding. It is also possible to export a GFF with GO terms. For further details, link here.
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 2: OmicsBox General preferences
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.
Figure 3: Wizard to configure the OmicsBox update behaviour
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.
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.
Figure 4: Proxy settings dialog
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.
OmicsBox allows to automatically and continuously save OmicsBox results after a certain amount of time.