Manuel Lera-Ramirez
Working on OpenCloning, an Open Source web application to plan and document cloning.
opencloning.org
Open Source in science enthusiast. Previously PomBase, yeast genetics, image analysis and cytoskeleton.
- Working on a tool to define Golden Gate syntaxes for #OpenCloning. You define your syntax, and then you can drag-and-drop your plasmids in OpenCloning, they will be sorted into the right categories, and you can do combinatorial assembly. Reach out if you'd like to contribute: syntax.opencloning.org
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- yarn install not working due to @cloudflare.social #outage :(
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- 🚀 A long-requested feature just landed in #OpenCloning 🔬🧬 You can now manually annotate sequences and create primers right from the editor ✨ Hope it makes your workflow a bit smoother! 📨 If you want to stay updated with upcoming features, subscribe to the mailing list (link in the comments)
- #OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software ✅ Free 🔓 Open Source 🧬 More cloning methods than SnapGene 🤖 Can be automated with python 👨🔬 Built by a researcher — for researchers! 👉 Check it out at opencloning.org
- There is also a mailing list if you want to stay updated with the latest changes: eepurl.com/h9-n71
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- ✨ Last week at #ESSL2025 I presented a poster on #OpenCloning 🧬 🔥 Crowd favorite feature: pull gene sequences directly from NCBI — no copy-paste needed! 🎥 Here’s a quick demo 🔗 Visit opencloning.org
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- 🧬 Are you a wet lab scientist doing cloning or DNA engineering, or a bioinformatician curious about molecular biology? 🌱 Passionate about Open Source and Open Science? Join the pydna hackathon: dtu.events/pydnahackath... 🌱 Whether you're new to Python or an expert, there's a place for you!
- 🚀 OpenCloning now has a documentation page! Whether you're getting started or diving deep, find everything you need to make the most of OpenCloning, including a powerful search function to quickly find exactly what you’re looking for. #OpenCloning #OpenSource #SynBio 🔗 docs.opencloning.org
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[Not loaded yet] - 🔬 I added a template for the #GoldenPiCS #MoClo kit to #OpenCloning! ⚡ Speed up your design when cloning in #Kphaffii! 🧪 Simulate plasmid assembly 🧬 …and integration into the genome! 👉 Check it out here: opencloning.org 🌍 🎥 youtu.be/BadWzLjojb4
- Reposted by Manuel Lera-RamirezA paper I have been working on with Oliver Lemke in the Ralser lab has just come out: www.nature.com/articles/s41... We used predicted structures to gain insight into the evolution of metabolic proteins in yeast. A bit more in this linked-in post (www.linkedin.com/posts/benjam...).
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- Reposted by Manuel Lera-RamirezReposting as I hear about a German Pubmed-like initiative: let's build on Europe PMC which is already great
- Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes *all* bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed
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- Reposted by Manuel Lera-RamirezI got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Non-model Bioeng Custom Lab Hardware Turn Key Genetic Design Please repost for reach 💚
- 🚀 Just added support for Cre/Lox recombination to hashtag#OpenCloning! 🧬✨ 👇 Check out an example showing excision of a plasmid from a locus and re-integration using classic LoxP sites. 👉 Try it here: opencloning.org 🎞️ Demo video: www.youtube.com/watch?v=n0he...
- 🧬 If you are in London and you want to learn about a free & Open Source SnapGene/Benchling alternative that also supports automation 🤖, come to our next London Synbio Network meeting this Thursday 24th in Imperial!🎓 🎤 I’ll be giving a talk about #OpenCloning! events.humanitix.com/copy-of-lond...
- Come join us for the next London Synbio Network meeting on Thursday the 24th of April in Imperial. I am giving a talk about #OpenCloning, so join if you want to hear more about Open Source and automation of DNA engineering.
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- You can now ✅ verify your #OpenCloning sequences using sequencing data 🧬 (Sanger or Nanopore). Just load your files 📂 and see where they align! 🎯 #OpenCloning is free & Open Source, and supports most cloning methods! 🔬🛠️ 👉 Try it here: opencloning.org 🎞️ Demo video: youtu.be/n0hedzvpW88?...
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- #OpenCloning now displays primer details! 🧬🔍 Minimal info is shown in the table, and the full #primer3 report when clicking the ℹ️ icon. 🧪 The values in parenthesis are for the full primer, the preceding ones for the annealing part. 🔗 Try it yourself: opencloning.org 🎥 Demo: youtu.be/-wjOY4i6mjg
- Come join us this Thursday at 18:00 in UCL for 2 SynBio talks followed by networking over drinks. bsky.app/profile/lond...
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- 100% guilty of this myself as someone who is not mobilised, but this quote naively captures how our job as researchers often alienates us from our role as citizens. Focused on our research, and often uprooted and far from home we don't get involved until it is too late.
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- With #OpenCloning, you can very quickly access your locus of interest from the #NCBI to start cloning. No more downloading entire genomes and cutting your fragment of interest!
- 🧬🔬 Ever wondered if there’s a #GateWay plasmid in @addgene.bsky.social with GFP and the att sites you need? 🤔✨ Wonder no more! 🚀 Visit GateWayMine to search a database of #AddGene plasmids by feature or site type! 🧪🔍 🔗 gatewaymine.netlify.app More context in the thread! 🧵👇
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- 🧬 Now you can access @sevaplasmids.bsky.social directly from #OpenCloning ✨. 🔗 try it: opencloning.org 🎞️ demo: youtu.be/n0hedzvpW88?...
- I have turned the primer designer of #OpenCloning into a stepper after feedback from lab members and @francescodb.bsky.social. It now conveys more clearly the workflow. Below an example of #primerDesign for #GatewayCloning 🔗 try it: opencloning.org 🎞️ demo: www.youtube.com/watch?v=n0he...
- 🚀 #ShareYourCloning rebrands to #OpenCloning 🧫 An Open Source web application to plan and document molecular cloning 🧬 and genome engineering 🦠. Latest version adds support for WekWikGene 🔍 as a plasmid source, and UI improvements. 👉 Check it out here: opencloning.org 🌍
- A tutorial on how to design Gibson Assembly primers in #ShareYourCloning www.youtube.com/watch?v=GhBH... Try it at shareyourcloning.org
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- The new POMBOX kit is now available from @addgene.bsky.social To plan your cloning with this and other Golden Gate kits, you can try the kit template in #ShareYourCloning 🔗 Visit shareyourcloning.org 👉 Go to Templates > Moclo 🎞️ Full demo video www.youtube.com/watch?v=n0he... #pombe #MoClo
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