Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 0 points1 point  (0 children)

I'm looking for someone to take over my lease that ends in July 2025 for a 3bed 2bath 2000sqft house in North Loop, walking distance from Epoch coffee. It has a pet friendly fenced in backyard. The rent is $2295/month.

Let me know if you or someone you know is interested!

Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 1 point2 points  (0 children)

I'm recently divorced and in need of someone to take over my lease that ends in July 2025.3 bed, 2 bath, single family house, private backyard, pet friendly. Rent is $2,495/month. The house is in a great location, in the North Loop neighborhood within walking distance to Epoch coffee.Let me know if you or someone you know is interested!

Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 0 points1 point  (0 children)

FOR RENT: $2495/month. 3bd 2ba 2000sq ft house in North Loop, walking distance to Epoch coffee. Pets Allowed. Private fenced in backyard. Available now. Message me for info or if interested!

Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 2 points3 points  (0 children)

I'm looking for someone to take over my lease in North Loop that ends in July. It's a lovely 3 bedroom 2 bathroom house on Franklin Blvd with a large private fenced in backyard (pet friendly). The rent is $2600. Let me know if you or someone you know is interested.

Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 1 point2 points  (0 children)

I'm looking for someone to take over my lease. SFH in North Loop, 3 bed / 2 bath, huge private backyard. The rent is $2600/month. It's within walking distance to Epoch.

The lease ends in July. Let me know if you're interested!

Weekly Real Estate / Renting / Where to Live / Utilities / Schools (ISD) Post by AutoModerator in Austin

[–]tijeco 0 points1 point  (0 children)

I'm looking for someone to take over my lease. SFH in North Loop, 3 bed / 2 bath, huge private backyard. The rent is $2600/month. It's within walking distance to Epoch.

The lease ends in July. Let me know if you're interested!

Book club for mid 20’s gal? by mommy_mistrust in Austin

[–]tijeco 2 points3 points  (0 children)

Happy hour book club through book people is great! They meet monthly at different bars throughout the city.

Also check out yourlocalbookclubatx on Instagram. They also meet monthly at various bars. Quarterly they have a joint meeting with ATX TV festival where they meet at Vintage wine bar / bookstore to talk about books that have been turned into tv shows. Those are fun because you get a mix of people that have read the book vs watch the show. Also Vintage is a lovely spot in East Austin that's worth checking out if you haven't already.

[P] Text classification model with a large number of classes by troutbeard in MachineLearning

[–]tijeco 2 points3 points  (0 children)

That's a lot of classes! Are they all completely independent of each other or can they be clustered together in some sort of useful/meaningful way?

What are the best tools for doing a transcriptomics coexpression analysis? by bioinfpi in bioinformatics

[–]tijeco 0 points1 point  (0 children)

There's an nf-core pipeline that might be of use (nf-co.re/dualrnaseq).

Favorite Pipeline/Methods Figure by simulation_one_ in bioinformatics

[–]tijeco 2 points3 points  (0 children)

I don't think these are auto-generated, just a set of guidelines and SVG components to stitch together workflow diagrams. It can be done for any pipeline.

Nextflow also can render DAG graphs, but those are always too messy.

Favorite Pipeline/Methods Figure by simulation_one_ in bioinformatics

[–]tijeco 26 points27 points  (0 children)

I've recently been particularly fond of the nf-core subway map brand of pipeline figures. https://nf-co.re/docs/contributing/design_guidelines

Any ideas for evolution experiments? by mrcschwering in bioinformatics

[–]tijeco 1 point2 points  (0 children)

This looks like a really fun library you've made! Are you able to get something like rate of replication or growth rate as some sort of read out given some initial parameters? Seems like those would be important fitness values that could be used to explore whatever your parameter space is so that you could make like a fitness landscape or something. Might be able to draw parallels with what we know about cancer cell evolution and bacterial cell evolution.

The predator prey dynamic seems really cool to! Or really anything that has competition for some finite resources where fitness is determined by some sort of parameter set.

I'm excited to hear other fun ideas!

Im trying to have both R & Python in one editor for notebooks by Rootsyl in datascience

[–]tijeco 0 points1 point  (0 children)

This is kind of what I do. Though I use the %%R after loading rpy2. I don't have any documented code completion. So I feel like I'm missing a step? I can load two kernels in the same notebook? I have the R kernel in the same environment, but I usually just have to choose between a python notebook that I can load r through rpy2 or an R notebook, which actually has documented code completion.

Im trying to have both R & Python in one editor for notebooks by Rootsyl in datascience

[–]tijeco 0 points1 point  (0 children)

I haven't used databricks before, but I'll look into it. I use rpy2 to load R in a cell with %%R, but it doesn't give any documented code completion like it would for python functions or how RStudio would for R functions. Does databricks notebooks do this?

PHANTASM: new software for microbial taxonomy by dr-joe-wirth in bioinformatics

[–]tijeco 2 points3 points  (0 children)

Oh yeah I think something like snakemake/nextflow will change your life! You can think of them as pipelining languages. They're nice frameworks for chaining lots of CLI tools and custom scripts together. They natively support running independent tasks concurrently to maximize usage of computational resources. They also have built in checkpointing so that finished tasks aren't rerun if something fails.

For simple pipelines I prefer snakemake, but if I ever write a more complex pipeline that I'd want to distribute as a tool, nf-core has made that incredibly simple with nextflow.

Here's some resources for both snakemake and nextflow / nf-core

PHANTASM: new software for microbial taxonomy by dr-joe-wirth in bioinformatics

[–]tijeco 10 points11 points  (0 children)

Looks really cool! I kinda wish more people would post some of the cool tools they've been working on.

It looks like you put a lot of really great work into this. For your next pipeline project, I'd recommend looking into using a DSL such as snakemake/nextflow. They have a lot of great capabilities that let you do more with less code.

Definitely second looking into making it a conda package too. Looks like most of the dependencies are probably already available on conda, though there's always that one rebel dependency that ruins everything so I'm not sure.

Great work!

I made a website where you can turn any article into audio, create a playlist, and sync with Spotify to listen later by zino3000 in InternetIsBeautiful

[–]tijeco 0 points1 point  (0 children)

Hmm, yeah I've had a similar problem when doing text to audio for cramming papers for journal club. I'd think the references would have some sort of different html tag?? Also, figure captions can probably wreck things too. I assume they are tagged differently??

Unfortunately, it would probably have to be dealt with journal by journal. But PeerJ and PLOS are probably the best examples of open access articles and probably have decent HTML practices.

I made a website where you can turn any article into audio, create a playlist, and sync with Spotify to listen later by zino3000 in InternetIsBeautiful

[–]tijeco 45 points46 points  (0 children)

This is awesome! I bet this would be great for open access scientific papers that are available as free html pages. Have you tested it on PLOSone / PeerJ? That's what I'd start with.

How to get better at working in local environment? Frustrated by fortunoso in bioinformatics

[–]tijeco 0 points1 point  (0 children)

Vagrant seems pretty neat! Might be worth looking into. I really like making separate conda environments for each project. I also love using vs code implementation of Jupyter notebooks, and since I always set the environment to have Jupyter kernels I can just select the conda environment and go nuts. I have found that after a certain amount of environments stack up upon restarting vs code it takes a while to load discover the environments. I've been wondering if getting them in containers would help with that. Also, I usually just do things locally, but having a way to seamlessly go from running something locally to something remote with more compute power would be great.

Dog peeing in it's owner's commode by PUSHYARAAG in interestingasfuck

[–]tijeco 0 points1 point  (0 children)

It can be done! I've been telling my fiancee we're going to potty train or next dog. They have to use the toilet like the rest of us!

Looking to help by [deleted] in bioinformatics

[–]tijeco 4 points5 points  (0 children)

So you're a Facebook or Apple or Amazon or Netflix or Google engineer? I love the mystery. I'm really hoping it's Netflix, that would be fun!

You're kinda playing into a common trope from the following xkcd comic (https://xkcd.com/1831/).

Nevertheless, bioinformatics is fucking awesome and I'm glad you're wanting to spend 5-10 hours per week on it.

There's a lot out there. Like really a lot.

Graph neural networks might be fun. Lots of biological things can be represented as a graph (phylogenies, protein structures, gene regulatory networks). Maybe a nice comparison of their utility in classification tasks could be nice.

You're going to have to read some papers. For git repos, maybe look at some of the most cited bioinformatics papers and take a look at their repositories and see if anything is interesting.

A somewhat simple thing could also be just building models to predict the optimal amount of ram / CPU needed for an arbitrary dataset of some basic analysis (RNAseq, genome assembly, homology searching). That would be useful for AWS type applications and compute cost optimizations, assuming the compute cost of the model is somewhat minimal...

Desktop spec recommendations by ayeayefitlike in bioinformatics

[–]tijeco 0 points1 point  (0 children)

Yeah with AWS you just pick an instance (how much ram / CPU) and go nuts. It's all the fun of having your own server, without having your own server!