Frequently Asked Questions¶

Common questions about BioRemPP usage, results, and operations.

General¶

What is BioRemPP?¶

BioRemPP is a web service for functional inference of bioremediation potential from KEGG Orthology (KO) identifiers.

Do I need an account?¶

No. BioRemPP is open and does not require login.

Is BioRemPP free?¶

Yes. The service is free for scientific and educational use.

It is not usable for commercial product claims without experimental confirmation.

Input and Validation¶

What input format is accepted?¶

A plain text (.txt) file:

>Sample1
K00001
K00002

Rules:

sample header starts with >
KO format must be K#####
no blank lines between sample blocks

What are the default limits?¶

max samples: 100
max KO identifiers: 500,000
max upload size: 5 MB

These limits can be tuned per deployment.

Can I use an example file?¶

Yes.

Homepage card Need a KO Input Example? -> Download Example
or Use Example Data in the upload section

Processing and Job ID¶

What is the Job ID generated after processing?¶

A unique identifier for each processing execution in the format:

BRP-YYYYMMDD-HHMMSS-XXXXXX

It lets you restore the same processed result without reprocessing.

Where can I find and copy my Job ID?¶

After processing success (Step 2 feedback)
In /results overview card, with copy action/icon

How long is a Job ID resumable?¶

By default, up to 4 hours after processing (TTL-based, configurable by deployment).

Resume by Job ID¶

How does Resume Analysis by Job ID work?¶

From the homepage panel:

enter your Job ID
click Resume
app restores payload and redirects to /results

Why does resume require the same browser profile?¶

For security isolation, resume ownership is bound to the browser context that created the job.

Why does Resume by Job ID fail?¶

Common causes:

invalid Job ID format
expired TTL window
different browser profile/context
temporary block after many failed attempts (rate limit)

If resume is unavailable, reprocess the file to generate a new Job ID.

Results and Interpretation¶

What do BioRemPP results represent?¶

They represent genetic potential inferred from KO presence.

They do not directly prove:

gene expression
enzyme activity
in situ degradation performance

Are empty database results an error?¶

Not necessarily. Empty sections can happen when uploaded KOs do not map to that specific database scope.

Data Retention and Privacy¶

Is data stored permanently?¶

No. BioRemPP uses temporary server-side cache for processing and resume.

What is retained and for how long?¶

Processed payloads are retained temporarily (default 4h) and purged automatically after expiration.

Is data shared between users?¶

No. Resume access is isolated by browser-bound ownership token and validation checks.

Technical Stack and Reliability¶

Is resume always backed by Redis?¶

Not necessarily. Deployments can use different cache backends while keeping the same user-facing behavior.

What if I close the tab/browser?¶

You may still recover the run within TTL using Job ID in the same browser profile.

What browsers are supported?¶

Recent versions of Chrome, Firefox, Edge, and Safari are recommended.

Citation and Licensing¶

How do I cite BioRemPP?¶

Use the current citation templates in How to Cite.

Can I use BioRemPP commercially?¶

Software and data licenses define permitted reuse, but commercial product claims require independent experimental confirmation.

See Terms of Use and License.

Downloads¶

What can I export?¶

integrated database tables (CSV, Excel, JSON)
use-case-level tables
chart images (PNG, SVG, JPEG)

Does export filename include Job ID?¶

Current naming is timestamp-based. Job ID is shown in the UI for tracking/resume.