PADLOC

PADLOC news & updates | | | Managed by @leighton_payne & @SimonJacksonNZ

[PADLOC @padlocbio]

Hard to believe it's been 2 years since we released PADLOC v1.0.0 😱. To celebrate, here's a new major release – 📦 PADLOC v2.0.0, with lots of new systems! 🔥 (available from GitHub/Conda and the PADLOC web server: https://t.co/pD0FML84aq) 🧵 1/n

[Leighton Payne @leighton_payne]

🚨📄PREPRINT ALERT! "New antiviral defences are genetically embedded within prokaryotic immune systems" ⚔️🦠 #phage https://t.co/qmNNM51uHY

[PADLOC @padlocbio]

N.B. PADLOC-DB v2.0.0, including all the new and exciting candidate systems, is only compatible with PADLOC v2.0.0, so make sure you update both! 🧬💻

[PADLOC @padlocbio]

Some users are having issues with older versions of conda not installing padloc v2.0.0 by default, to avoid this you can specify padloc=2.0.0 during installation. If you're experiencing similar installation issues, please drop a comment on this thread 😀: https://t.co/bJZaG8mag5

[PADLOC @padlocbio]

'Nough said! 😤 Go hunt those defence systems! 🛡🦠⚔️ #phage

[PADLOC @padlocbio]

Hard to believe it's been 2 years since we released PADLOC v1.0.0 😱. To celebrate, here's a new major release – 📦 PADLOC v2.0.0, with lots of new systems! 🔥 (available from GitHub/Conda and the PADLOC web server: https://t.co/pD0FML84aq) 🧵 1/n

[PADLOC @padlocbio]

As always, we're open to additions and corrections to our models, data attributions, etc., so please get in touch with @padlocbio, @leighton_payne, or @jacksonlabnz via Twitter, email us, or open an issue on GitHub if you have suggestions! 🥰 6/n

[PADLOC @padlocbio]

[1] https://t.co/Pz3XXWrkJz
[2] https://t.co/l1EtcrORrI
[3] https://t.co/he0YFNvATh

[PADLOC @padlocbio]

Check out the updated web server! Now w/ RM systems (finally!) 😍, new systems from Rousset et al. (1) 🤹, darTG from LeRoux et al. (2) 🎯, Gasdermins from Johnson et al. (3) 🛡️, and added functionality to identify the ncRNA (msr-msd) components of retrons 😱. #phage 🔥🦠⚔️

[PADLOC @padlocbio]

The PADLOC webserver is back in action with a bunch of updates - thread to follow later. Please report any bugs.

[PADLOC @padlocbio]

We're planning to upgrade the PADLOC webserver tomorrow (starting in ~18 h), so will be temporarily offline or there might be a few bugs we didn't pick up on the dev server. Apologies in advance for the inconvenience - we'll be back with more #phagedefense systems and features.

[Leighton Payne @leighton_payne]

📦PADLOC v1.1.0 and PADLOC-DB v1.3.0 are now available for download, bringing the CLI version of PADLOC up to date w/ the web server 💻(i.e. new #phage defence systems 🛡️⚔️and optional #CRISPR array integration). Update your install w/ #conda. Happy Valentine's Day! 💘💝❤️‍🔥

[PADLOC @padlocbio]

User uploads and results are stored anonymously on the server (assigned random filenames) until either the user deletes the job, the session expires, or for 10 days (whichever happens sooner). Feedback and bug reports are always welcome.

[PADLOC @padlocbio]

*Server error* Hi all, due to a mix up with our server maintenance system, all users results run prior to ~4 hours ago are currently unavailable. The result pages load but the output figure, table and downloads fail. We're working to fix this, apologies for the inconvenience.

[PADLOC @padlocbio]

Results for all jobs uploaded in the February have now been recomputed. However, the CRISPR array detections could not be rerun. Hopefully not too much of a pain for anyone!

[PADLOC @padlocbio]

PS. new jobs should be unaffected and we're hoping to retrieve the older outputs tomorrow.

[PADLOC @padlocbio]

Bug update: since the addition of CRISPR arrays to PADLOC @RobFagerlund noticed the annotation .gff import to Geneious was broken. This has now fixed and files should work with the drag-drop import.