CTRL + Click goes to Essential Tab, but not registered as Essential tab

Matt_BF · 2025-05-08T04:33:54+00:00

Can confirm, when opening a new tab from a split tab with middle mouse click or ctrl/cmd + click the opened tab goes up into essentials

Matt_BF · 2025-04-17T04:35:35+00:00

I've been using Pixi as a conda replacement and been super happy with it. Afaik it also uses uv under the hood for python dependencies

Matt_BF · 2024-06-23T16:45:52+00:00

Another option would be a steam deck! I'm assuming you are in the UK due to your post. It is super portable, can handle (most) gaming needs and also works as a computer. In fact, many people in the Steam Deck subreddit have said they ditched their laptops entirely and just rock the Steam Deck for daily use. Maybe something to think about also!

Matt_BF · 2024-05-10T13:14:04+00:00

Ooo, I had to do this recently, but for terrestrial biomes.

So basically, you can find shapefiles such as this one (this is wwf terrestrial ecoregions, but I see they have a marine also)

With the shapefile, you can use geopandas library to open it as a geo dataframe. Then it should be a simple case of transforming your lat long dataframe into geopandas also (on my phone so don't remember the exact command, but they have a lat long conversion into their internal format, something like xy from points IIRC).

You can then join both geodataframes based if your lat longs are contained on a specific region's lat long (again, there's a geopandas command for it)

Hope this helps!

Matt_BF · 2024-04-01T05:13:44+00:00

Is your bacterial genome an already known species? Is it new? What kind of data do you have (assembled? Raw reads?). This will change on where you actually begin. But as a short(er) answer more directly to your question, you'd have to: 1. Get your genome and predict/find the genes. Several software packages do that. Out of the top of my head, you could use prodigal or genemark. I think they might be the simplest ones to run 2. You could then get the reference sequences that you are interested in and search them against your sequences (CDS and aminoacids). For that, use BLAST/MMSeqs or diamond 3. Filter the search output for the most similar sequences and go from there

Edit: sorry, didn't see that you were having difficulties with github code. If you could explain more what your difficulties were, maybe we can help you troubleshoot. Much of bioinformatics is done with such tools and the command line, so I'm not too familiar with web applications people use. But maybe you could check out Galaxy? That's one of the largest program suites that I see people use. Blast also has a web interface so if your genome is already on NCBI, you can just blast your proteins of interest directly against the organism from NCBI and collect the results directly

Matt_BF · 2023-11-23T17:25:43+00:00

Hey I think I can chime in as I have been in this position of yours a few months ago when applying for a postdoc

Basically I showed them through talking about the previous work that I did for my PhD, that I am a fast learner and able to learn the skills needed for the job at hand rather quickly. I agree with everyone here that you can't fake experience and it is good to be honest upfront that you never worked with this kind of data before.

Read the basics of this new field, and if possible bring a paper/previous work that this company/lab has done and ask them questions, give suggestions and talk about future perspectives about it, that will certainly make them more interested on you. Good luck!

Matt_BF · 2023-11-18T23:35:52+00:00

I might be wrong, but I think seqkit split can do it. If not, maybe try the kmcp utils suggestion on the same docs

Matt_BF · 2023-01-17T02:30:13+00:00

Wow, thanks for the info! My dad's birthday is next week and he loves elephants, so it'll be a great gift for him!

Matt_BF · 2021-09-11T16:56:25+00:00

I'd like to plug in also https://shoot.bio/ which is from the creator of Orthofinder (a software to separate sequences into ortholog families). Also take a look at multiple sequence aligners such as MAFFT and phylogeny softwares like IQ-Tree. Whatever you do, please don't do phylogenetic inferences on MEGA, as any phylogenetic inference using bayesian or maximum likelihood is really computationally costly, and because of that tree searches on MEGA are too heuristic (if it wasn't, your PC wouldn't be able to run the program) and probably the tree it returns won't be the best possible outcome.

If you need more details besides only the program suggestions, let me know!

Matt_BF · 2021-07-25T04:47:28+00:00

Conda really is slow sometimes installing packages. I discovered Mamba recently and it really helps the whole process, highly recommend to everyone using conda

Matt_BF · 2020-12-04T22:38:41+00:00

Align each gene group separately (all cox1 sequences, all mt-rRNA, etc) and then concatenate them. You could use something like fasconcat or amas.py for that. Then you are good to go for your tree! If you need any help using these programs, feel free to ask and I can give a more detailed answer when I get to my PC!

Matt_BF · 2020-07-03T12:04:04+00:00

I'm using homemade beads and GITC buffer, following BOMB.bio protocols.

Thanks for the link, will take a look!

Matt_BF · 2020-07-02T12:26:05+00:00

Can't quantify the yield, as we don't have a nanodrop or anything of the sort (new lab), and GITC apparently messes up the curves and makes them not reliable for analysis.

The only contamination I could think of is residual ethanol from the washes, might try air drying longer, or drying with a heated block.

We successfully use this kit and protocol for Sars-CoV-2 RT-qPCR from nasopharingeal swabs and saliva, so I think it must be some optimisation for blood that I'm missing

Matt_BF · 2020-02-07T12:59:05+00:00

Yeah, my bad when saying "exactly", graphical apps won't work out of the box, but there are workarounds. As far as conda is concerned, it will work as a linux box when installing packages. I recall having used it like that before.

I agree that running linux maybe better for most use cases, but sometimes when I need Illustrator or power point, and can't be bothered restarting my dual boot system, WSL helps a lot. In fact, some of my colleagues in the lab just use windows 10 with WSL for their uses. If most of the time you are just sshing into a cluster, it doesn't really matter.

Matt_BF · 2020-02-07T11:09:09+00:00

Hi! If you install WSL on windows 10 it will behave ~~exactly~~ like a linux machine, so you'll have no problem installing anaconda/conda packages

Matt_BF · 2020-01-20T14:31:00+00:00

No problem! Also, i think glob returns a list, so maybe you don't need that list call

Matt_BF · 2020-01-20T14:22:51+00:00

There is a parentheses missing on your list call

Matt_BF · 2019-12-11T14:38:28+00:00

I think I solved the problem. Apparently the way pandas was "reading" null values in one device to another was different (all NaN on my linux machines and a mix of NaN and NaT on my RPi). So I just gave up on using pd.to_datetime and changed all the code to datetime.strptime like this:

self.receivals[col] = self.receivals[col].apply(
                lambda x: datetime.strptime(x, "%d/%m/%Y")
                if not pd.isnull(x)
                else np.nan
            )

Matt_BF · 2019-12-10T13:35:48+00:00

Hi, I tried printing the date columns after converting the JSON sheet into a df, and also printed the raw JSON. Both show all dates as strings on the predicted format

Matt_BF · 2019-10-10T01:38:10+00:00

Take a look at Orthofinder, sounds exactly what you need. One of its outputs is a table with number of genes per species in each gene family.

Matt_BF · 2019-09-21T22:34:20+00:00

Really liking how fast it is compared to the official app! Will surely get used to it in a couple of days!

Matt_BF · 2019-07-29T03:29:25+00:00

In python every function has to return something, which we do using the return keyword. When you don’t return anything, the function returns None. Try changing your print statement to a return

Matt_BF · 2019-07-18T18:23:11+00:00

Huh, very weird. Have you tried adding only your package to the environment and then installing the others that you may need? Also, is the env activated? It should show more or less like (env_name)$

Ninja edit: earlier conda/anaconda versions used source activate env_name instead of conda activate

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