Structural

Cryo-EM, from moviesto a 3D model

Scipion on an Ubuntu desktop of your own.RELION, Xmipp, EMAN2 and CTFfind, behind one GUI.

Scipion 3.8.34 cores · 64 GBNVIDIA GPUOpens in a browser tab

hub://scipion

$ dxflow workflow create --identity scipion hub://scipion --start --link

01Pick a machinecores, memory and a rate per hour

02Create the workflowpulled from the hub, once

03Run it, then stopstopped when the work is done

The application

One project,many packages

RELION, Xmipp, EMAN2 and CTFfind, driven from one place.

The whole pipeline

Imports, motion correction, CTF, picking, classification, refinement.

Plugins on demand

The core is installed; the rest arrive from the plugin manager later.

It asks for a lot

An NVIDIA card, 64 GB and fast storage, because the data is enormous.

How you run it

Every defaultis one override away

The session reads its settings from the environment, so you set them on the start line.

VNC_PASSWORDWhat the tab asks for. It ships as dxflow, and everyone reading this knows that.

PANEL and TASKBARThe panel stays, the taskbar goes. Scipion opens a window per step, and the panel is how you find them again.

The data directoryScipion's user data is linked into /volume, so projects and results outlive the machine.

start it your way

$ dxflow workflow start scipion --override env.app.VNC_PASSWORD=something-long

$ dxflow workflow start scipion --link

The session

The project manager,and all it opens

The panel is kept, so Scipion's windows are easy to arrange.

6082Browserin the tab, at /vnc.html

5901VNCin a native client

/volumeStoragemovies, projects, results

Open it from anywhereStart with --link and the session comes back on an HTTPS address.

Set a password firstVNC_PASSWORD defaults to dxflow, and everyone can read this page.

Good to know

The core is here,the plugins come later

Scipion installs itself; the packages it drives are pulled in from the plugin manager when you ask for them.

Plugins install on demand

Xmipp, RELION and MotionCor2 are fetched and built the first time you enable them. Leave room in the plan for that.

It wants everything

A card, plenty of cores, a lot of memory and fast disk. Cryo-EM reconstruction is not a small machine's job.

The usual order

Import, motion correction, CTF, picking, 2D and 3D classification, refinement, then post-processing.

The image

Pulled once,then it stays

Scipion arrives as one image. This is what comes down the first time, and what the disk should have free for it.

1.8Gamd64compressed, the way the registry counts it

100GOn diskunpacked, with room to work beside it

ghcr.io/dxflow-ai/scipion:latestPublished from the hub, pulled on the first start and kept for the ones after it.

amd64 onlyOne architecture is published, so pick a machine that matches it.

What it asks for

What it wants,and what it needs

The definition asks for 4 cores and 64 GB. The image comes up on less than that, and a start given --fit trims the ask to whatever the machine actually has.

4 cores · 64 GBAsks forwhat the definition writes down

2 cores · 32 GBRuns onthe least the image comes up on

NVIDIAGPUrequired, and filtered for

The ask is not the floorThe definition writes down what suits the work. The image itself starts on less, which is what the second figure is.

--fit caps it to the hostA start given --fit trims each step to what the machine actually has, for that start alone. The definition is never rewritten.

Machines that fit it

Scipion asks for 4 cores and 64 GB, with an NVIDIA GPU. Cheapest first.

G2 Standard-16

$1.43/ hour16 cores · 64 GB · NVIDIA L4Start this machine

G4dn 4XLarge

$1.51/ hour16 cores · 64 GB · Tesla T4Start this machine

NC16as T4 v3

$1.51/ hour16 cores · 110 GB · Tesla T4Start this machine

Run Scipion on your own machinePick a machine that meets it, and it opens about a minute after you ask.

Start Scipion Browse workflows