Clarence Mah
@clarencemah.me
CompBio Scientist, PhD • #spatialomics, #rnabiology, #opensource • Chinese-Malay American
🍱 Creator of github.com/ckmah/bento-tools
⭐️ clarencemah.me
🍱 Creator of github.com/ckmah/bento-tools
⭐️ clarencemah.me
Glad to be part of such an open and collaborative community pushing #SpatialBio forward! Thanks for inviting and hosting us @kevinyamauchi.bsky.social @lucamarconato.bsky.social & Giovanni Palla 🙏
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
January 20, 2025 at 8:11 PM
Glad to be part of such an open and collaborative community pushing #SpatialBio forward! Thanks for inviting and hosting us @kevinyamauchi.bsky.social @lucamarconato.bsky.social & Giovanni Palla 🙏
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
Reposted by Clarence Mah
Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
December 19, 2024 at 10:17 AM
Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
Oof, software releases are always so nerve racking 😅 just updated bento-tools.readthedocs.io to v2.1.4 🥳
We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️
We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️
December 18, 2024 at 10:13 PM
Oof, software releases are always so nerve racking 😅 just updated bento-tools.readthedocs.io to v2.1.4 🥳
We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️
We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️
This looks amazing! Really appreciate the focus on documentation and usability.
Very pleased to announce that our package for Multiscale Spatial Analysis - MuSpAn - has landed!
The preprint is on biorxiv now, but you can find a lot more details at www.muspan.co.uk, including documentation, worked tutorials (an ever-expanding list), install guides, and how to get the code!
The preprint is on biorxiv now, but you can find a lot more details at www.muspan.co.uk, including documentation, worked tutorials (an ever-expanding list), install guides, and how to get the code!
December 11, 2024 at 3:01 PM
This looks amazing! Really appreciate the focus on documentation and usability.
that's a lot of git commits
New on NBC News : “After years on the rise, ‘All I Want for Christmas Is You’ listenership is slipping”
After years on the rise, ‘All I Want for Christmas Is You’ listenership is slipping
www.nbcnews.com
December 7, 2024 at 3:58 PM
that's a lot of git commits
I'm not in NLP or javascript, but found compromise.cool is a very cool example of "less is more" ❤️ #opensource
December 1, 2024 at 8:52 PM
I'm not in NLP or javascript, but found compromise.cool is a very cool example of "less is more" ❤️ #opensource
Reposted by Clarence Mah
Sign of the times, no more bluebird on the biorxiv engagement tab..
November 24, 2024 at 9:59 AM
Sign of the times, no more bluebird on the biorxiv engagement tab..
Hey science folks 🧪! Trying to stay on top of #SpatialBiology convos, tech, studies, conferences, etc.? Well here's a feed for you!
bsky.app/profile/did:...
bsky.app/profile/did:...
November 21, 2024 at 3:54 PM
Hey science folks 🧪! Trying to stay on top of #SpatialBiology convos, tech, studies, conferences, etc.? Well here's a feed for you!
bsky.app/profile/did:...
bsky.app/profile/did:...
oof, this was probably inevitable with the status quo. but also eLife's impact factor would simply drop over time to reflect the "lower quality" if it really is the case. seems like a hasty decision by Clarivate. 🧪
www.science.org/content/arti...
www.science.org/content/arti...
Open-access journal elife will lose its ‘impact factor’ over controversial publishing model
Web of Science index decides to strip key metric because elife’s unusual peer review doesn’t meet its criteria
www.science.org
November 15, 2024 at 6:33 PM
oof, this was probably inevitable with the status quo. but also eLife's impact factor would simply drop over time to reflect the "lower quality" if it really is the case. seems like a hasty decision by Clarivate. 🧪
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by Clarence Mah
Restarting a previous discussion on here:
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
November 15, 2024 at 10:27 AM
Restarting a previous discussion on here:
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
Reposted by Clarence Mah
This is hard to hear. A lot more cuts to Federal science funding are likely in the offing. We need to find new/better/more ways to drive interdisciplinary collaboration and cooperation in science 🧪
What a horrible day again, 2nd time this year. Slowly finding out which of our colleagues have been let go, we have lost some good people from the Science Division today 🧪😢 💔 www.space.com/nasa-jpl-lay...
NASA's Jet Propulsion Lab laying off 5% of its workforce
About 325 JPL employees are being let go.
www.space.com
November 15, 2024 at 12:35 AM
This is hard to hear. A lot more cuts to Federal science funding are likely in the offing. We need to find new/better/more ways to drive interdisciplinary collaboration and cooperation in science 🧪
Now that more of the spatial community is here, I've put together a feed for #SpatialBiology! Check it out here:
bsky.app/profile/did:...
Also, if you think it's missing posts, msg me the post and I'll see how I can improve things 🧪🖥️🧬
bsky.app/profile/did:...
Also, if you think it's missing posts, msg me the post and I'll see how I can improve things 🧪🖥️🧬
November 14, 2024 at 9:24 PM
Now that more of the spatial community is here, I've put together a feed for #SpatialBiology! Check it out here:
bsky.app/profile/did:...
Also, if you think it's missing posts, msg me the post and I'll see how I can improve things 🧪🖥️🧬
bsky.app/profile/did:...
Also, if you think it's missing posts, msg me the post and I'll see how I can improve things 🧪🖥️🧬
cue Python vs R 🧪
For this to really look like ~2015 Twitter, we need the following:
1) Discussion about postdoc salaries in the US
2) Discussion about how many hours per week should a tenure-track prof work (in the US)
3) Lior fighiting with Manolis
4) Michale Eisen fighting Elsevier
1) Discussion about postdoc salaries in the US
2) Discussion about how many hours per week should a tenure-track prof work (in the US)
3) Lior fighiting with Manolis
4) Michale Eisen fighting Elsevier
November 14, 2024 at 9:03 PM
cue Python vs R 🧪
Reposted by Clarence Mah
Safety of these individuals is also a concern of mine, as I’ve mentioned on another thread 🥲
But as we expand our own networks with new voices, hopefully we can brainstorm together how to protect everyone from harm 🧠 These online spaces are communities, and we gotta look out for one another 💕
But as we expand our own networks with new voices, hopefully we can brainstorm together how to protect everyone from harm 🧠 These online spaces are communities, and we gotta look out for one another 💕
In addition to the change in ✨ good vibes ✨, I’m also concerned about how starter packs might make individuals (especially minorities) easier to potentially target 🥲
Hopefully there’s a quiet opt-out or “starter pack invitation” feature in the future? 😅
Hopefully there’s a quiet opt-out or “starter pack invitation” feature in the future? 😅
November 12, 2024 at 3:43 AM
Safety of these individuals is also a concern of mine, as I’ve mentioned on another thread 🥲
But as we expand our own networks with new voices, hopefully we can brainstorm together how to protect everyone from harm 🧠 These online spaces are communities, and we gotta look out for one another 💕
But as we expand our own networks with new voices, hopefully we can brainstorm together how to protect everyone from harm 🧠 These online spaces are communities, and we gotta look out for one another 💕
So.. according to this umap, what cell type are you? 🧬🖥️
November 11, 2024 at 9:01 PM
So.. according to this umap, what cell type are you? 🧬🖥️
Agreed, reminder to myself to be mindful of inclusivity, biases and echo chambers when curating my own feed.
💡Related; I'm putting together a #spatialbiology starter pack, please let me know if you would like to be included!
💡Related; I'm putting together a #spatialbiology starter pack, please let me know if you would like to be included!
Starter packs are a great way to find people. But I followed a few tech/AI starter packs, and now have a sizeable gender skew in who I'm following.
To counteract, I started collecting this list. Who else should I be following & add? 👇 go.bsky.app/LaGDpqg
To counteract, I started collecting this list. Who else should I be following & add? 👇 go.bsky.app/LaGDpqg
November 11, 2024 at 1:34 PM
Agreed, reminder to myself to be mindful of inclusivity, biases and echo chambers when curating my own feed.
💡Related; I'm putting together a #spatialbiology starter pack, please let me know if you would like to be included!
💡Related; I'm putting together a #spatialbiology starter pack, please let me know if you would like to be included!
Reposted by Clarence Mah
Genomics, evolution, and more starter pack!
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
November 10, 2024 at 8:27 PM
Genomics, evolution, and more starter pack!
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
Reposted by Clarence Mah
Another helpful resource for people to check out is @clearsky.app by @thieflord.dev: clearsky.app 🌐✨
You can use the site to look up who’s blocking a user 🛑, who that user is blocking 🙅🏽♀️, any lists the user is a part of 👥, and their message history (if authorized) 🦋!
You can use the site to look up who’s blocking a user 🛑, who that user is blocking 🙅🏽♀️, any lists the user is a part of 👥, and their message history (if authorized) 🦋!
November 10, 2024 at 9:22 PM
Another helpful resource for people to check out is @clearsky.app by @thieflord.dev: clearsky.app 🌐✨
You can use the site to look up who’s blocking a user 🛑, who that user is blocking 🙅🏽♀️, any lists the user is a part of 👥, and their message history (if authorized) 🦋!
You can use the site to look up who’s blocking a user 🛑, who that user is blocking 🙅🏽♀️, any lists the user is a part of 👥, and their message history (if authorized) 🦋!
Great list of curated individuals in the space! Though I recommend checking out who exactly is included 🧐 you can either "follow all" or follow accounts individually
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Genomics+Bioinformatics Starter Pack 🧬🖥️
Join the conversation
go.bsky.app
November 10, 2024 at 4:14 PM
Great list of curated individuals in the space! Though I recommend checking out who exactly is included 🧐 you can either "follow all" or follow accounts individually
Thanks for all the recent follows, I'm happy to see many familiar faces 😊
I'd like to briefly introduce myself here. I am a #bioinformatics scientist in #SanDiego building methods for #spatialbiology. I love building open source tools for the community and am excited to meet all of you!
I'd like to briefly introduce myself here. I am a #bioinformatics scientist in #SanDiego building methods for #spatialbiology. I love building open source tools for the community and am excited to meet all of you!
November 10, 2024 at 2:19 PM
Thanks for all the recent follows, I'm happy to see many familiar faces 😊
I'd like to briefly introduce myself here. I am a #bioinformatics scientist in #SanDiego building methods for #spatialbiology. I love building open source tools for the community and am excited to meet all of you!
I'd like to briefly introduce myself here. I am a #bioinformatics scientist in #SanDiego building methods for #spatialbiology. I love building open source tools for the community and am excited to meet all of you!