Connecting instruments with Porta

Getting a qPCR run into analysis software usually means exporting on the instrument PC, then copying that file to a memory stick or emailing it to yourself. Porta is a small program that runs on the instrument PC and makes the folders you choose visible inside Clarida, so you can import a run straight from where the instrument wrote it. On a Roche LightCycler 480 it can go further and read finished runs from the instrument itself, with no export step. This page covers what it does, how you use it week to week, and how to set it up.

Porta is a small program you install on your instrument PC. Once it is running, the export files your instrument software writes appear as a list inside Clarida, so you can import a run without copying it to a memory stick or emailing it to yourself.

Nothing about your run changes. The instrument software writes its export exactly where it always did, and you still export it the way you do now. Porta only changes how that file reaches Clarida.

Two things worth knowing before you read further. Porta runs on Windows only, which is where instrument PCs generally live. And for most instruments it reads files: it fetches the export your software produces, rather than talking to the instrument itself. The exception is the Roche LightCycler 480, where Porta can read runs from the instrument's own database with no export step; there is a section on that below.

Your IT department may want to look at this before you install it. Everything they usually ask (what it connects to, what it can reach, how it is built) is written up at Porta, notes for IT review. That page is public, so you can send them the link without their needing a Clarida account.

You tell Porta which folders it may read, typically wherever your instrument software drops its exports. From then on, inside Clarida you can:

• Browse those folders as a file list, without leaving the application.
• Import a run file straight from them into an experiment.

A file is read only when you ask for it, then handed to the ordinary importer described in Importing instrument data. Same Cq export, same column matching, same reconciliation against your design. Porta changes where the file comes from, not what happens to it afterwards.

It only ever reads. Your original files are never moved, renamed, or changed, and Porta never uploads anything on its own initiative.

Because Porta calls out to Clarida rather than the other way round, there is usually nothing for IT to open up: no firewall rule to request, no port, no VPN. In practice that often means you can install it without filing a ticket and waiting.

Run your plate as you always do and export the Cq table from the instrument software. Wait until the instrument software says the run has finished. qPCR instruments write their file as they go, so an export grabbed early is a half-finished run. Porta cannot tell the difference, but you can.

Then, from your own computer, open the experiment in Clarida and go to Import & annotate.

This is the one place your habits change. Before you had a connector, clicking the drop zone opened your computer's own file browser straight away. Now it asks first: a Where are your Cq files? list appears, with This computer at the top and each connected machine below it. Choosing This computer gives you the familiar file browser, exactly as before. Choosing a connector browses the instrument PC instead.

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Connectors are listed as connector name, folder label, so a machine sharing two folders appears twice. Each shows whether it is currently online.

Pick a connector and you get a file list from that machine, with sizes, and a .. entry for stepping through subfolders. Tick as many files as you want and import them in one go, the same way you would multi-select in your own file browser. Files are listed alphabetically, which for most instruments means date-stamped exports fall into chronological order on their own.

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From there the import proceeds exactly as it would if you had uploaded the files by hand, and each one keeps its original name and timestamp.

What this removes is the middle of the journey: no memory stick, no emailing an export to yourself, no wondering whether the copy on your laptop is the current one. The instrument PC does need to be switched on and connected when you import, which is worth knowing if your lab powers instruments down overnight.

If something looks wrong. A connector showing offline almost always means that PC is off, asleep, or off the network. It reconnects by itself once the machine is reachable, and nothing needs restarting. A connector missing from the list altogether has usually not had any folders added to it yet, and a file missing from a folder you can see is probably in a neighbouring folder nobody has added. Files above 25 MB are refused, which is comfortable for qPCR exports and a real limit for digital PCR.

Five steps, no command line, about ten minutes.

Before you start: a Windows PC that can see your export folders, administrator rights on it (as for installing any Windows program), and an internet connection on that machine.

Steps 1, 4 and 5 you do in Clarida from your own computer. Steps 2 and 3 you do sitting at the instrument PC.

1. Create a connector in Clarida

In the sidebar, go to Library → Connectors and choose New connector.

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Name it after the machine it will run on. PC159_Quantstudio is more useful in six months than Connector 1, and this name is what you will be picking from when you import.

Clarida then shows you a one-time enrollment code and your workspace address. Leave the panel open; you need both in step 3. The rest of the panel walks you through the same steps as below.

2. Install Porta on the lab machine

Download the installer from the same panel and run it on the instrument PC. It installs a background service that starts automatically, so it survives a reboot without anyone logging in.

Windows will warn you, and the way past it is not obvious. You will see "Windows protected your PC", describing Porta as an unrecognised app. The first dialog offers only Don't run. Click More info and a Run anyway button appears, along with the publisher: Clarida.

That warning is about familiarity, not safety. The installer is signed by us, which is why Windows can name Clarida as the publisher rather than showing "Unknown". SmartScreen also tracks how widely a particular file has been downloaded, though, and a newly released version has no such history yet. You will see it again after each Porta update, for the same reason.

3. Pair it with your workspace

On the lab machine, press Start, type Clarida, and open Clarida Porta connector setup. This opens a small page served by Porta on that machine itself. It is not a website, and it is not reachable from anywhere else on your network.

Paste in the enrollment code and workspace address from step 1. The connector pairs, and back in Clarida it changes from Awaiting pairing to Online.

4. Choose what it may read

A newly paired connector serves nothing at all until you say so. From the connector's panel in Clarida, add the folders it may read, and give each one a label you will recognise later.

Name the specific export folder rather than a whole drive. Porta cannot read anything outside the folders you name, so a narrow choice is safer, and a folder with forty thousand files in it is unpleasant to browse.

On a machine attached to a LightCycler 480, this is also where you point Porta at the instrument itself, so it can read runs without an export. Reading a LightCycler 480 directly, below, covers what to fill in. The two are independent: a connector can serve folders, the instrument, or both.

5. Try it

Open any experiment, start an import, and check that your connector's folders show up as a source. If they do, you are finished. If the connector still reads Awaiting pairing, step 3 did not complete.

On a Roche LightCycler 480 there is a second option: Porta can read finished runs out of the instrument's own database, so there is no export step at all. You pick the run by name inside Clarida and it comes across directly.

This uses Roche's LIMS Interface Module, which is part of the LightCycler 480 software but is not always installed. If it is missing, ask whoever supports the instrument to add it; nothing on the Clarida side can substitute for it.

What to fill in

The connector's panel in Clarida asks for four things:

• LIMS server computer — the machine running the LightCycler 480 software, which Roche calls the control unit. Use localhost if that is the same machine Porta is installed on. Otherwise give its computer name or IP address. This is a real machine on your network, not a label you choose, and not the name of the database or the experiment.
• Port — 1776 unless someone changed it. Roche's module also uses 1777, so both need to be open if a firewall sits between the two machines.
• LC480 login — an account in the LightCycler 480 software. Roche recommends creating a separate account used only for this, rather than the System Admin login.
• Password — for that account. This is sent to the lab machine and stored only there. Clarida never keeps a copy, which is why it cannot be shown back to you later.

Save, then use Test connection. That signs in and reports what happened, so you find out about a wrong password or an unreachable machine now rather than the first time someone tries to import.

To change the password later, type a new one. Leaving it blank keeps the one the lab machine already has, so editing something unrelated will not disturb a working connection.

One connection at a time

The LIMS server accepts a single connection, and Roche's default is not to raise that. In practice this means Porta and the LightCycler 480 software's own LIMS features cannot both be signed in at once: whichever gets there first holds it, and the other is told the connection limit is reached.

Porta is built for this. It signs in only for the moment it needs, then signs out, so it is not sitting on the connection between imports. If you do see a connection-limit message, something else is signed in; close it and try again.

A run also has to be finished before it can be read. A run still in progress is not offered.

On a shared instrument, a core-facility machine, or a PC managed by your IT group, the person responsible for that machine has the final say. Anyone with access to it can switch folder sharing off from Porta's own setup page, and nothing done in Clarida will turn it back on.

That is deliberate, so nobody can widen what a machine shares without the people who run it knowing. It is worth a short conversation before you install Porta on an instrument you do not look after yourself.

Uninstall Porta from Settings → Installed apps, as with any Windows program. This removes the background service and deletes the connector's credential from the machine, so nothing is left behind that could reconnect.

Separately, revoke the connector in Clarida to close its record. Revoking does not need access to the machine, which makes it the right action for a PC that has been lost, replaced, or decommissioned.

Upgrading to a newer version clears nothing. You will not have to pair the connector again.

More instruments read directly. The LightCycler 480 is the first instrument Porta reads without an export step. Others will follow, each needing its own manufacturer interface, so they arrive one at a time rather than all at once.

More than one instrument per connector. An LC480 connector is configured for a single instrument today. Labs running two would need a connector for each.

Larger files. Digital PCR runs reach hundreds of megabytes, well past what the current transfer path handles, so those need different plumbing.

What Porta does today is what the top of this page says. It reads the folders you choose — and, on a LightCycler 480, the runs themselves — when you ask, so a run gets from the instrument PC into your analysis without the trip in between.