Jack Nicoludis

structural biology, computational biophysics, genomics, ML/AI |🏳️‍🌈 (my own posts and opinions)

[PRX Life @PRX_Life]

KnotFold enables AlphaFold2 to correct mispredicted connectivity patterns in disulfide-rich peptides by mutating conserved cysteine residues in multiple sequence alignments to simulate protein coevolution.

Read the paper: https://t.co/nWIKQTA6jG

#MLSB @workshopmlsb

[Jack Nicoludis @_jackn_]

@sfboehner @Trevor4SF What was factually incorrect? Also, you clearly have never biked in the city. No cyclists is going to bike up the massive hill on dolores (or Church, Guerrero) than on very flat Valencia. Also, Valencia is a major place to shop and eat, cyclists want to go there.

[Jack Nicoludis @_jackn_]

@sfboehner @Trevor4SF You said church is “safer.” Why is Valencia unsafe for cyclists? Most cycling accidents are caused by drivers not following the rules of the road -> they are breaking the law. Let’s enforce road laws

[Jack Nicoludis @_jackn_]

@sfboehner @Trevor4SF Safety from what? Are you saying it is a cyclist’s responsibility to protect themselves from people breaking the laws? Or should we make laws and enforce them so that people don’t injure others?

[Jack Nicoludis @_jackn_]

@sfboehner @Trevor4SF people bike to stores and restaurants on valencia. Church has the muni - muni tracks can be a hazard for bikes. It is also more hilly than Valencia. Why not block Valencia off to cars and have cars drive on Guerrero - it already has two lanes each way and no bike lane.

[Jack Nicoludis @_jackn_]

@Shenanigans_ATL @Polonius_SF @Trevor4SF Why can’t Valencia be one way? By not having two way car traffic you could accommodate more parking, have parklets and bike lanes. I guess the struggle would be getting SFFD on board, but they could use the bike lane as they do now. Divert traffic to Guerrero

[Jack Nicoludis @_jackn_]

@Trevor4SF I dislike the center bike lane because it has created unusual traffic patterns that encourage bad behavior in both drivers and cyclists. But having cyclists weave between restaurants and the parklets seems like it will discourage cyclists from using it…

[Jack Nicoludis @_jackn_]

@Trevor4SF I’m not sure I understand the “floating” parklets. Does that mean the bike lane will be between the restaurant and the parklet such that pedestrians will be frequently crossing it? That seems dangerous and inconvenient for cyclists. It will make pedestrians angry with cyclists.

[Luke Bornheimer (Streets Forward) @LukeBornheimer]

@BetterValencia Also noting that the person biking fell into the travel lane where, if there was a car/truck driving there, they would have been run over and potentially killed.

Sandwiching people between two lanes of driving cars/trucks is a dangerous idea, and this bikeway should be replaced.

[Luke Bornheimer (Streets Forward) @LukeBornheimer]

The Valencia center bikeway is causing head-on collisions between people, resulting in serious injuries.

Mayor Breed and SFMTA should replace the center bikeway with curbside protected bike lanes or pedestrianization immediately.

Please take action now: https://t.co/d8C2LqqBsz

[Jack Nicoludis @_jackn_]

I’ll be at @workshopmlsb at #neurips2023 this Friday and have a PhD internship position in my group this coming summer. Say hi if you are interested! https://t.co/7sY3yovTXW

[Jack Nicoludis @_jackn_]

Can I simultaneously hate the Valencia center bike lane while also doubting that the removal of parking spaces on Valencia caused 80% loss of a business on Valencia? Let’s make Valencia one way with a protected bike lane and lots of parking spaces and loading zones!

[The San Francisco Standard @sfstandard]

San Francisco's Amado's Bar Closes, Blames Valencia Bike Lane

The San Francisco bar owner said the Valencia Street center-running bike lane forced him to close and is killing small businesses. https://t.co/56MhnVy8Rx

[valencia4people @valencia4people]

Thanks @SFMTA_Muni. Your design is working as intended.

[Jack Nicoludis @_jackn_]

@sokrypton There are open source variant effect predictors that perform worse than AlphaMissense, so wouldn’t the responsible thing be to release the best model to the public?

[Jack Nicoludis @_jackn_]

Ok, so who is going to train OpenMissense to get them to change their (deep)minds about this?

[Sergey Ovchinnikov @sokrypton]

Interesting excuse... 🤔 hopefully this is not the start of closed source software in the field...

"As part of our commitment to releasing our research breakthroughs safely and responsibly, we will not be sharing model weights, to prevent use in potentially unsafe applications."

[Jack Nicoludis @_jackn_]

@slushbumps @LukeBornheimer @BetterValencia love this idea!

[Jack Nicoludis @_jackn_]

@drdre4000 @mary_munson4 Christian Anfinsen went to Swarthmore to get a chemistry degree!

[Luke Bornheimer (Streets Forward) @LukeBornheimer]

What happens to the Valencia Street center cycle track when a vehicle obstructs the driving lane? Exactly what you expect.

This wouldn’t happen with curbside protected bike lanes (@BetterValencia), which are better for safety, business, and climate.

Please end the “experiment.”

[Jack Nicoludis @_jackn_]

@jjschultz @gamescan @SFMTA_Muni I don’t have big issues with the idea of a center lane. My issue is the implementation has been horrible, the lane isn’t protected at all, the curbs are dangerous for cyclists, and there’s no engineering controls for drivers who won’t obey rules (left turns, entering bike lane)

[Luke Bornheimer (Streets Forward) @LukeBornheimer]

SFMTA insists that people on bikes “share the road” with cars on Valencia while SFMTA installs its unprotected center cycle track that’s supposedly “closed.”

I followed SFMTA’s guidance; look and see what it got me.

The center cycle track is flawed; the rollout is almost worse.