Manuel Lera-Ramirez
@manu-lera.bsky.social
Working on OpenCloning, an Open Source web application to plan and document cloning.
https://opencloning.org/
Open Source in science enthusiast. Previously PomBase, yeast genetics, image analysis and cytoskeleton.
https://opencloning.org/
Open Source in science enthusiast. Previously PomBase, yeast genetics, image analysis and cytoskeleton.
Pinned
#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
✅ 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
🚀 Update from @pombase.bsky.social!
Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨
To get started with OpenCloning, check the docs: docs.opencloning.org
Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨
To get started with OpenCloning, check the docs: docs.opencloning.org
February 11, 2026 at 6:12 PM
🚀 Update from @pombase.bsky.social!
Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨
To get started with OpenCloning, check the docs: docs.opencloning.org
Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨
To get started with OpenCloning, check the docs: docs.opencloning.org
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
syntax.opencloning.org
January 28, 2026 at 6:55 PM
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
syntax.opencloning.org
Reposted by Manuel Lera-Ramirez
I got a plasmid map from another lab as *.dna file 🧪. The SnapGene program can open it. I do not want to install their "free" viewer in my linux system. The solution: OpenCloning opencloning.org . With it, I loaded the .dna file and downloaded the sequence plus a nice map. Thanks OpenCloning team 🤩
OpenCloning
An Open-Source web application for DNA engineering
opencloning.org
November 27, 2025 at 7:53 PM
I got a plasmid map from another lab as *.dna file 🧪. The SnapGene program can open it. I do not want to install their "free" viewer in my linux system. The solution: OpenCloning opencloning.org . With it, I loaded the .dna file and downloaded the sequence plus a nice map. Thanks OpenCloning team 🤩
yarn install not working due to @cloudflare.social #outage :(
December 5, 2025 at 9:02 AM
yarn install not working due to @cloudflare.social #outage :(
Reposted by Manuel Lera-Ramirez
Looks definitely worth a try for cloning
#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
✅ 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
November 26, 2025 at 6:41 PM
Looks definitely worth a try for cloning
OpenCloning
An Open-Source web application for DNA engineering
opencloning.org
November 26, 2025 at 9:01 AM
🚀 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)
🔬🧬 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)
November 26, 2025 at 9:01 AM
🚀 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)
🔬🧬 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)
There is also a mailing list if you want to stay updated with the latest changes: eepurl.com/h9-n71
November 25, 2025 at 11:40 AM
There is also a mailing list if you want to stay updated with the latest changes: eepurl.com/h9-n71
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
#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
✅ 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
November 24, 2025 at 5:04 PM
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
cc: crisprflydesign.bsky.social
bsky.app/profile/manu...
cc: crisprflydesign.bsky.social
#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
✅ 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
November 24, 2025 at 5:03 PM
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
cc: crisprflydesign.bsky.social
bsky.app/profile/manu...
cc: crisprflydesign.bsky.social
If you are looking for an Open and free alternative to SnapGene, with a more modern look than ApE, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
#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
✅ 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
November 24, 2025 at 5:01 PM
If you are looking for an Open and free alternative to SnapGene, with a more modern look than ApE, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
#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
✅ 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
November 24, 2025 at 4:59 PM
If you are looking for an Open and free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
If you are looking for an Open and Free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
#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
✅ 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
November 24, 2025 at 4:59 PM
If you are looking for an Open and Free alternative to SnapGene, you may want to give #OpenCloning a try!
bsky.app/profile/manu...
bsky.app/profile/manu...
#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
✅ 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
November 24, 2025 at 4:57 PM
#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
✅ 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
Reposted by Manuel Lera-Ramirez
Hope to see you all next week!
t.co/4tHIVGUJzc
t.co/4tHIVGUJzc
November 24, 2025 at 11:32 AM
Hope to see you all next week!
t.co/4tHIVGUJzc
t.co/4tHIVGUJzc
Reposted by Manuel Lera-Ramirez
Lead the future of Synthetic Biology and empower your regional community.
2026 iGEM Community Recruitment is now open!
- Become an iGEM Ambassador
- Lead as a Project Head
Deadline: Nov 24, 2025 (23:59 UTC)
Apply here: community.igem.org/recruitment/2026
2026 iGEM Community Recruitment is now open!
- Become an iGEM Ambassador
- Lead as a Project Head
Deadline: Nov 24, 2025 (23:59 UTC)
Apply here: community.igem.org/recruitment/2026
November 3, 2025 at 4:24 PM
Lead the future of Synthetic Biology and empower your regional community.
2026 iGEM Community Recruitment is now open!
- Become an iGEM Ambassador
- Lead as a Project Head
Deadline: Nov 24, 2025 (23:59 UTC)
Apply here: community.igem.org/recruitment/2026
2026 iGEM Community Recruitment is now open!
- Become an iGEM Ambassador
- Lead as a Project Head
Deadline: Nov 24, 2025 (23:59 UTC)
Apply here: community.igem.org/recruitment/2026
Reposted by Manuel Lera-Ramirez
New paper alert!!
Led by Lucas, we automated all the design steps for genome engineering experiments in streptomycetes. If you are using our Streptomyces CRISPR toolbox, you can now design hundreds of experiments in a matter of minutes.
@tilmweber.bsky.social @kblin.bsky.social
....
Led by Lucas, we automated all the design steps for genome engineering experiments in streptomycetes. If you are using our Streptomyces CRISPR toolbox, you can now design hundreds of experiments in a matter of minutes.
@tilmweber.bsky.social @kblin.bsky.social
....
StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes
Streptomycetes hold immense potential for discovering novel bioactive molecules for applications in medicine or sustainable agriculture. However, high-throughput exploration is hampered by the current Streptomyces genetic engineering methods that involve the manual design of complex experimental molecular biological engineering strategies for each targeted gene. Here, we introduce StreptoCAD, an open-source software toolbox that automates and streamlines the design of genome engineering strategies in Streptomyces, supporting various CRISPR-based and gene overexpression methods. Once initiated, StreptoCAD designs all necessary DNA primers and CRISPR guide sequences, simulates plasmid assemblies (cloning) and the resulting modification of the genomic target(s), and further summarizes the information needed for laboratory implementation and documentation. StreptoCAD currently offers six design workflows, including the construction of overexpression libraries, base-editing, including multiplexed CRISPR-BEST plasmid generation, and genome engineering using CRISPR-Cas9, CRISPR-Cas3, and CRISPRi systems. In addition to automating the design process, StreptoCAD further secures compliance with the FAIR principles, ensuring reproducibility and ease of data management via standardized output files. To experimentally demonstrate the design process and output of StreptoCAD, we designed and constructed a series of gene overexpression strains, and performed CRISPRi knockdowns in Streptomyces Gö40/10, underscoring the tool’s efficiency and user-friendliness.. This tool simplifies complex genetic engineering tasks and promotes collaboration through standardized workflows and design parameters. StreptoCAD is set to transform genome engineering in Streptomyces, making sophisticated genetic manipulations accessible for all and accelerating natural product discovery.
pubs.acs.org
October 16, 2025 at 2:59 PM
New paper alert!!
Led by Lucas, we automated all the design steps for genome engineering experiments in streptomycetes. If you are using our Streptomyces CRISPR toolbox, you can now design hundreds of experiments in a matter of minutes.
@tilmweber.bsky.social @kblin.bsky.social
....
Led by Lucas, we automated all the design steps for genome engineering experiments in streptomycetes. If you are using our Streptomyces CRISPR toolbox, you can now design hundreds of experiments in a matter of minutes.
@tilmweber.bsky.social @kblin.bsky.social
....
✨ 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
🔥 Crowd favorite feature: pull gene sequences directly from NCBI — no copy-paste needed!
🎥 Here’s a quick demo
🔗 Visit opencloning.org
September 22, 2025 at 10:46 AM
✨ 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
🔥 Crowd favorite feature: pull gene sequences directly from NCBI — no copy-paste needed!
🎥 Here’s a quick demo
🔗 Visit opencloning.org
Reposted by Manuel Lera-Ramirez
🎉 London SynBio Network is back! Join us on 25th of September.
🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski
💐 Open Flower: designer flowers for art and education
Nick Desnoyer
➡️ Register at: events.humanitix.com/london-synbi...
🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski
💐 Open Flower: designer flowers for art and education
Nick Desnoyer
➡️ Register at: events.humanitix.com/london-synbi...
London SynBio Network 10
London SynBio afterwork talks and networking event on Thursday 25th of September
events.humanitix.com
September 17, 2025 at 2:31 PM
🎉 London SynBio Network is back! Join us on 25th of September.
🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski
💐 Open Flower: designer flowers for art and education
Nick Desnoyer
➡️ Register at: events.humanitix.com/london-synbi...
🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski
💐 Open Flower: designer flowers for art and education
Nick Desnoyer
➡️ Register at: events.humanitix.com/london-synbi...
🧬 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!
Join the pydna hackathon: dtu.events/pydnahackath...
🌱 Whether you're new to Python or an expert, there's a place for you!
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
August 13, 2025 at 5:11 PM
🧬 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!
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
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
August 7, 2025 at 7:53 AM
🚀 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
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