Project creation and scaling-up

One of the main goals of INSaFLU is to make data integration completely flexible and scalable in order to fulfill the analytical demands underlying laboratory surveillance throughout each flu epidemics. As such, INSaFLU allows users to create several projects (each one including multiple user-selected samples) and add more samples to each one as needed. In a dynamic manner, project outputs (e.g., gene- and genome-based alignments and phylogenetic trees) are automatically re-build and cumulatively updated as more samples are added to each project. The outputs are provided to be compatible with multiple downstream applications.

Creating and scaling-up a project

Within the Projects menu:

1. Go to Projects menu and choose Create project

You are encouraged to create “umbrella” projects, such as projects enrolling same sub-type viruses from the same season that will be compared with the vaccine reference virus for a given flu season.

You can designate the projects so that the name easily indicates the combination “virus sub-type/season/reference” (e.g. A_H3N2_2017_18_vaccine_ref)

_images/create_project_1_create.png

2. Choose a Project Name, select a Reference sequence and Save

Important

You should select a reference sequence (e.g., the vaccine strain from the current influenza season) that fits both your amplicon design (i.e., a multi-fasta file containing the set of reference sequences with the precise size of each “intra-amplicon” target sequence that you capture by each one of the RT-PCR amplicons) and the set of samples that will be compared (e.g., same sub-type viruses from the same season to be compared with the vaccine reference virus).

_images/create_project_2_name_ref.png

3. Add the samples to be included in the project

_images/create_project_3_add_samples.png

Samples are processed immediately upon selection, so, at this time, users may start monitoring the Project progress by checking the number of samples in the following status: Processed (P); Waiting (W) and Error (E).

_images/monitoring_project_status.png

4. Scale-up your project.

You may add more samples to your Project project at any time.

_images/create_project_4_scale_up.png

5. Remove samples from your project.

You may want to remove some samples from your project (e.g., for exclusively keeping samples with success for all 8 locus)

_images/create_project_5_remove_samples.png

Monitoring Projects’ progress

INSaFLU projects are automatically run upon creation. So, at this time, users may start monitoring the Project progress by checking the number of samples in the following status: Processed (P); Waiting (W) and Error (E).

_images/monitoring_project_status.png