#bioinfo

[problemeule]

some poor soul is crying in the library

[purrfectly]

forgot my backpack at the bar last night. if i have more than 1 beer i WILL leave anything and everything behind

[sparklingstudycare]

100 days productivity challenge

Day 14

July 29

Academics:

Studied immunology at library- 1.5 hour

Studied PTC at library- 1 hour

Studied bioinfo at home- 1 hour

Studied immunology at home- 30 mins

Diagrams etc- 30 mins

General:

Read few chapters of My Journey by A.P.J Abdul Kalam

Exercise- 20 mins

Skipping-10 mins

Had coffee

Ate fruits

Laundry

Skincare

10 mins walk after dinner

[pencil-peach]

G Witch Onscreen Text: Episode 5

Part SEIS of my attempt to transcribe and discuss all the text that appears on screens and tablets in G Witch, because I got that dog in me! This is episode 5, "Reflection in an Icy Eye"

<< Episode 4, if you so dare.

Till and Suletta Boiled Eggs Indulgence.

Shall we begin?

TEXT: WINNER PILOTING DEPARTMENT KP003 ELAN CERES F/D-19 ZOWORT 7 WINS 0 LOSS 0 TIE

At the end of Elan's 3 v 1 duel, we get a look at the Zoworts ID and the fact that he has 7 wins and no losses.

When Bel is speaking to the Peil witches, we get another look at Aerial's profile. What's new here are the terms on the bottom right, those being

PMET LINK PMET SUBLINK BIOINFO LINK PILOT DATA LINK MS DATA LINK INTEGRATED PMET LINK

I could not tell you what any of these mean, BUT I have recorded them for convenience.

The text on Nuno's tablet is very difficult to make out, but we can for sure read CONTROL SYSTEM on the header at the top, so we know that's what he's looking at here. I'll give my best guess as to what the 3 sub-headers say, from top to bottom.

I-MSEACTRL-SYS I-MSEECTRL-SYS 5011-ONCODE

If my transcription is right, the first two are probably meant to be read as something like I - MOBILE SUIT [EA/EE] CONTROL SYSTEM

I'm not as confident in the bottom one though, i think i have ONCODE correctly but I'm not sure if the first half is really 5011, which would be Aerial's Permet Code ID. But it's the only interpretation that makes sense to me because I can only read it otherwise as SETH-ONCODE. And I have my doubts about that one.

Some broader looks at Aliya's divination table

Of course, everyone and their mother would tell you this, but Aliyah points to the stone that landed on the Roman Numeral for 12, wondering if it represents 'a brother' of Suletta's. This is foreshadowing the Eri reveal, as Aerial + the Eri clones that pilot each one of its GUND Bits adds up to 12, meaning Suletta has 12 sisters.

Of course, the stone in the middle represents her mother, and Aliyah comments that it's very big.

I can't help but wonder if Miorine is represented somewhere here as well?

This scene is where we finally get to see the title of the book Elan is reading. As I stated before, this book is The World as Will and Representation (Translated in the show proper as The World as Will and Idea) by Arthur Schopenhauer. The importance of this book to understanding Elan's character cannot be overstated, and it's worthy of its own post, but simplified as far down as possible (and also acknowledging that I have yet to read the essay myself, it's long...I'll get to it though, I promise...)

The two most essential ideas of this work in their relation to Elan are that:

All human suffering and conflict is a result of the "Will" that exists within us: An ever striving force that pushes us to pursue our innermost desires.

In order to reduce the inherent pain and suffering that comes with life's cruelty, one can minimize their desires, and deny the force of their will.

In simpler terms, if you never desire anything from your life, even the idea of living itself, you will never be made to suffer from the lack of it.

From the shows beginning, we can see how Elan completely embodies this philosophy. He denies love, he denies his emotions, he never acts of his own accord, only following the orders he's been given by Bel and the Peil witches.

But that changes when he meets Suletta, because Suletta awakens within him one of his deepest desires. To find someone who is like him, someone who understands him.

But when he realizes that Suletta isn't an Enhanced Person, that he's still completely alone, he can't handle it.

Because he allowed himself to want for something, he invited suffering back into his life when it was something he was not allowed to have.

And now that he's opened his heart to desire, it's not something that can be closed. For the rest of our time with him, we see how this incident with Suletta has broken the spell. When he duels Guel, he tortures him. Shaddiq repeatedly acknowledges that there's been something different about him ever since he was with Suletta.

In the multiple scenes when Elan sees the candle of the birthday cake when he closes his eyes, the flame represents how his will has been relit. It's the flame of his desire. And despite his continued insistence that it doesn't exist, that he still doesn't want anything, doesn't need anything, the flame only keeps growing.

It sparks up when Suletta sings the birthday song to him.

And it all comes to a head during their duel. He immediately starts listing off the things Suletta has that he doesn't. Friends, family, a past and future, even hope. And laments that it's just not fair, demands to know why she can't let him have one thing.

When he fully accepts himself, and remembers the person who celebrated his birthday, he realizes that it was wrong to assume that he had nothing, and to continue to believe that he could never have anything.

But, tragically, in fully accepting his desire, he also had no choice but to accept the suffering that comes with it. And, well.

Yknow.

Anyway in this scene we can see the path that he wants Suletta to take in the testing sector.

We can see that Lauda's Dilanza is registered as such in Asticassia, and its ID code is MD-003 1L. Despite being registered as such, both Elan and Rouji refer to it as "Regolith" in this duel.

This is the Pharact's navigation system. At the bottom, the warning says: ALERT: MALFUNCTION JOINT SENSOR: ACTIVE MINOR DAMAGE FROM [???] STATIC ELECTRICITY.

We can see that the Pharact is showing that the static electricity is damaging its joints. This is where Elan gets the idea of how to defeat Guel.

TEXT: (top to bottom) ALERT DMG CTRL-SYS ON

MD-R-0099[?] RIGHT LEG - [???] DAMAGE

MD-O HEAT AXE - RECOVERED

This shows up on the display when Guel is hit by the Pharact's stun beams for the first time. Though my transcription might not be fully accurate, we can at least glean from this that mobile suit components seem to have their own internal codes used by their various systems. That's cool!

When Guel is immobilized by the static electricity, the warning on his screen reads ANAMOLY DETECTION

Bonus: When Guel first makes it through the stun lasers and approaches Elan, you can actually see the monitor start writing out "TARGET LOCKED" before cutting to the next scene.

They really must have had a whole team of people working on these UI elements and they REALLY gave it their all!

Anyway, that's all!! Sorry that this one kinda took a detour down the Elan train for a bit there! I always get carried away with these things...

Uhh as a reward.... hmm...

One time I saw Shaddiq referred to as "Malibu Sephiroth" and I've never been able to forget it. It's so real. God Damnit.

Click here to go to Episode 6! >>

Click here to go to the Masterpost!

[libraryofmoths]

Moth of the Week

Beautiful Yellow Underwing

Anarta myrtilli

The beautiful yellow underwing is a moth in the family Noctuidae. This species was first described in 1761 by Carl Linnaeus. They are predictably named for the yellow portion of the hindwings.

Description This moth has many color variations depending on region.

The most common coloration is a red and olive brown or olive yellow forewing with strong white patterning. Additionally, the forewings have a ringed stigmata (a spot by the middle of the forewing found on Nocuids) next to a distinctive white spot. The hindwings are orange-yellow with a dark brown borders.

In Sweden, northern England, and northern Scotland the forewings are instead a dull dark purple with paler patterning, the same triangular white spot, and a less visible stigmata. The hindwings are the same yellow-orange but with black borders.

Other minor differences are the forewing being mixed with olive brown in East Anglian, the red in the forewing being almost entirely switched with black in Hyères, France, and the forewing being mixed with black as well as a pale yellow hindwing in Sintra, Portugal.

Average wingspan: 21 mm (≈0.83 in)

Diet and Habitat This moth feeds on Heather and Bell Heather only. It can be found across Europe in Scandinavia, Britain, France, Germany, Switzerland, Spain, Portugal, Italy, and Russia. They prefer sunny habitats that grow heather easily such as heathland and moorland in the mountain and sandy areas.

Mating The beautiful yellow underwing usually has two generations per year from April to early September. The larvae hatch from their eggs, which are laid on heather, in July in the north and April in the south.

Predators This moth is parasitized by the flies Athrycia impressa, Campylocheta inepta, and Phryxe vulgaris while both are in their larval stages.

Fun Fact The beautiful yellow underwing flies mainly during the day but occasionally comes out at night.

(Source: Wikipedia, Butterfly Conservation, Pyrgus.de, BioInfo (UK))

[inkofamethyst]

June 21, 2024

Okay so I started working through some problems on a website I discovered called Rosalind. It's several bioinformatics coding challenges. Harder ones unlock as you complete easier ones. It's pretty fun! Each problem has taken progressively longer to complete, sure, but I'm really loving getting back into the problem-solving mode. The one thing is that they don't give you aaaaaany coding help or hints or suggestions, so that will probably make things really difficult down the line (the best way to learn!!! (I need to maintain optimism)). Currently (almost) everything has been within my skillset, so mostly string manipulation and simple operations, and even though all of my work was probably worth a combined five hours on the eight problems (only finishing seven because I couldn't figure out probability), they ultimately weren't too bad. This will probably be what I spend my time on in the office to keep my coding skill up when I have nothing else to do.

While I should probably be learning R... I simply don't want to right now. Maybe in July after I get back from home idk.

I've also started watching music theory lectures (as opposed to just the interactive online textbook thing), and I really enjoy them! The circle of fifths is really clicking now for the first time in my life lol. I might try to also use downtime in the lab to write out my scales since I have a better understanding of how they work (kinda). It presents the textbook content in a slightly different way which I kind of appreciate, and then I can take that perspective back to the online textbook exersizes which I do for a few minutes daily. When I go home (so very soon!!!) I'm going to have to bring out ol' girl Melody and try some things, I think.

On that note (hehe), I need to think of a name for my bass!! My flute is Melody, my sax is Jasmine, my uke is Lulu... which are admittedly not very creative but I think they got a little better over time :P (Melody because flutes play melody (I was twelve, okay?), Jasmine because saxes play jazz, and Lulu for Honolulu because ukes are from Hawaii). So I think that, in keeping with tradition, the name has to be a little cheesy. I have one idea, but I don't think it's clever enough.

I haven't been eating very well lately. I'm in the process of restocking my pantry. I think I sort of just.. ran out of steam for cooking for myself. So it's been an embarrassing amount of chef boyardee, uncle ben's, velveeta... but tomorrow, I'm shaping up! Meatball stroganoff. And I have a plan for future meals, so I'll keep an eye out for sales, etc etc. Gonna get restocked! I'm shaping up! Maybe tomorrow I'll go for a walk in the morning! Maybe before even picking up my phone! Who knows!

Today I'm thankful that it's cooling down!!!! And also for the rain :) And also that the pollen is gone!!!!! After a month of suffering it was suddenly just no longer blowing into my open window :D

wait one last thing, circling back, even though I want to give my brain a break from the bioinfo problems, I inherently still feel that I've left something undone, as in I started working on problem 7 but couldn't figure out the right formula to even do the probability by hand, and even though I want to give myself a full weekend break, my brain is still passively thinking about it because I feel as though I didn't come to a satisfying conclusion. i wasnt even supposed to finish problem 8 tonight but i couldnt let it go.

so i need a distraction.

crochet it is (I'm working on my vest! it is suuuuper cropped (I'm about 2/3 through the front panel right now) and I fear my tiddies will not make it in, but hopefully it will be done before I go home so I can block it and maybe fix it? [edit, two days later: the front was just wonky because this is the first thing I've crocheted in years and I hadn't figured out my tension yet; def gonna redo it i think]).

actual last thing: surprisingly, I'm actually actively working toward several goals. like i always set them, but the past couple of weeks have been a bit of a lull. now I just feel craaazy energized.

[jobrxiv]

Postdoc in computational genomics - Farabella Lab Istituto Italiano di Tecnologia ????JOB OPENING???? We are hiring #postdoc #compbio #MathBio #bioinfo! For more info, feel free to DM or visit https://farabellalab.org. See the full job description on jobRxiv: https://jobrxiv.org/job/istituto-italiano-di-tecnologia-27778-postdoc-in-computational-genomics-farabella-lab/?feed_id=81812 #3d_genomics #chromatin #computational_biology #genomic_data #non_coding_RNAs #ScienceJobs #hiring #research

[ab3c]

O Vozes AB3C está de volta com a Temporada 2. Nesta semana vamos conversar com as equipes que tocam os projeto DNA praQ? e Bioinfo Fora da Bolha. Não perca este episódio, acesse http://vozes.ab3c.org.br nesta quinta às 14:00. Esperamos você lá.

[biotational]

Learning Scanpy...

[Citations under the read more]

Scanpy is one of the first packages I installed. It was mentioned by my Research Supervisor (RS) and some other reference material I have read that I haven't posted to this blog yet. But Scanpy is used extensively in the bioinfo/comp bio world to create graphs and organize data. My primary goal is to go through Scanpy's tutorials with their default dataset and then analyze the dataset from a paper that one of my colleagues presented to us two Thursdays ago (7/11) (I didn't realize it was 7/11 and I didn't get a free slurpee...). Below is the link to the official Scanpy website's tutorials page. I will post a reference post with this same link, but for convenience I will also post it here:

Preprocessing and Clustering...

Copying and pasting the code included with this section of the tutorial and running it grants me these results, which match the tutorial:

I don't completely understand how it pulled the database it's using, but I'll figure it out once I complete the tutorial.

Quality Control...

Copying and pasting the code included with this section of the tutorial and running it grants me these results, which match the tutorial:

I wanted to play around with the values a bit and see what happened to how the data was displayed. If I change the jitter value in the block of code that creates the violin plots:

to 0.9, this is what my results were:

As expected, it spread out the values a little more. Cool! Ok changing it back.

Doublet Detection and Normalization...

This is where I encountered some problems. In order to detect doublets, scanpy uses the detection method scrublet, which is awesome sauce, but the command was not working for me.

I kept getting an error from the scanpy files in charge of scrublet. I thought maybe I was missing something from the package, since it said skimage is missing, so I reinstalled scanpy but nothing changed. On the tutorials page there's a note that talks about alternative methods for doublet detection, so if I don't find a solution I can resort to installing one of those. But, I'm going to see if anyone's posted about this issue.

Someone on stack overflow suggested to install scikit-image to fix it, so I did and it worked! skimage does sound like it comes from the scikit-image package. I thought it wouldn't work because the console was taking a while to process like it does when it's gonna give me an error, but nope!

No error and it even went ahead and did the normalization no problem. Awesome sauce!

Feature Selection...

Got the same graphs as the tutorial, which means I'm on track. The tutorial says that this function:

annotates the genes by reproducing implementations of the specific methods depending on a chosen flavor. I'm not really sure what that flavor is or how I can pick it. I see a number value though so I'm gonna change it. Here's the graphs when I run this command with n_top_genes set to 5000.

Hmm... It didn't change anything, which is a shame. The program takes a lot of time processing the doublets so each time I execute the script again it takes a few minutes, which is not good for me because I love getting distracted while it's processing.

I'm changing the value back to 2000 and moving on, but definitely something to come back to and investigate.

Dimensionality Reduction...

Also got the same results as the tutorial, though my first graph displayed a little wider than the tutorial's graph. The first graph "gives us information about how many PCs [Principal Components] we should consider in order to compute the neighborhood relations of cells, e.g. used in the clustering function leiden() or tsne()."[1] It's better to overestimate than underestimate how many PCs. The second graph plots these PCs to "see if there are any potentially undesired features (e.g. batch, QC metrics) driving signifigant variation in this dataset."[1] According to the tutorial, nothing stands out as "too alarming", but the check was a good idea just in case there is anything that skews the data.

Nearest Neighbor Graph Construction and Visualization...

The only way for me to see the legend on the left side was if I stretched it out a bunch like this.

On the left is the output from the tutorial website, on the right is my output if I don't stretch it out. It's upside down? Each individual clump is pretty intact, but they're rotated different ways and in different positions than the tutorial reference image. I'm not sure what I did wrong, since I am just copying and pasting the code from the tutorial right now. I'm going to play around with it and see if I can fix anything later.

Clustering...

At first my console gave me an error but when I ran it again it worked just fine, so I'm not exactly sure what happened. But it looks like the tutorial sample image, aside from the clusters being in their new spots as shown by my previous figure. I also figured out how to fix how the graph looks, but I have to manually fix it each time. I'm planning to try to find out what can fix this, or at least what can set my defaults.

Re-assess quality control and cell filtering...

Same thing as above, seems to work just fine other than the fact that the clusters are in a different place from the tutorial examples.

[1] Dimensionality Reduction. Scanpy Preprocessing and Clustering Tutorial. https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering.html#dimensionality-reduction

[jobtendr]

(44) PhD, Postdoc and Academic Positions at Wageningen University & Research in Netherlands

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[soulmatefoundandlost]

ugh, i fkn hate bioinfo

[labis-unicamp]

🎉 Feliz Dia do Pi! 🥧 Hoje, celebramos uma das constantes matemáticas mais fascinantes e essenciais: o Pi (π). Com seu valor aproximado de 3.14159 , o Pi não é apenas um número que encontramos em cálculos geométricos, mas também um protagonista no campo da bioinformática. O Pi é utilizado em diversas ferramentas bioinformáticas para análise de dados biológicos, como sequências de DNA, RNA e proteínas. E por falar em proteínas, o estudo da estrutura das proteínas com o Pi ajuda a entender como elas funcionam e como podem ser manipuladas para o desenvolvimento de novos medicamentos. E aí tem algum outro exemplo de como o PI pode ser usado na Bioinfo? Compartilha com a gente.

[asdfint]

Nurturing brilliance, fostering collaboration #ICBB2024 🌱💡 #IntCongress at #Thailand #bioinformatics #biotechnology #biology #biotech #molecularbiology #genetics #science #biochemistry #microbiology #dna #research #genomics #medicine #immunology #bioinfo...

[sparklingstudycare]

Immunology- 1 and half hours

Molecular biology- one lecture

Genetics- one lecture

Probability- one lecture

Javascript- half an hour

Immunology- 1 hour

Bioinfo- 30 mins

Computational tools- 30 mins

[pencil-peach]

G Witch Onscreen Text: Prologue

I'm going to try my best to transcribe all of the (relatively important) text that appears on monitors and screens throughout the show, and talk about what they mean. Because they put WAY too much work into them just for them to be completely ignored. And also because I can.

More Under the Cut awooo awooOOooooOOOooo

TEXT: CONFIRM THRALL >>> LP-03

Not very important, clarifying communication is active between THRALL (Control) and LP-03 (Lfrith Prototype 03)

TEXT: PMET LINK REGRESSION TEST. INTERCONNECT

Device and Program Supporting Selection for Control Test

STATUS: READY

Just a Pre-Test status screen to make clear it's ready for the Permet Link Test

TEXT: GUND FORMAT [DISCONNECT] ERROR PHASE

Here we see the error message that's displayed when the Layer 33 Callback Test fails.

TEXT: PRESS BRIEFING: MS INVESTIGATION COMMITTEE OFFICIALS WARN ABOUT GUND FORMAT INTERPLANETRAY NEWS NETWORK

Here we see the news station (INN) reporting on the ongoing investigation by the Mobile Suit Investigation Committee into Ochs Earth and the Gund Format.

TEXT: (Top Left) SPACEFLIGHT OSTEOPENIA

(Bottom Left) MICROGRAVITY MUSCLE ATROPHY

(Top Right) SPACELIFE-ASSOCIATED NEURO-OCULAR SYNDROME

(Bottom Right) EQUILIBRIUM DISTURBANCE

(Middle) IMPAIRED SPATIAL ABILITY

(Bottom) HEALTH THREATS FROM COSMIC RAYS

This is a graph showing the various health risks humans suffer from prolonged exposure to cosmic rays in space, which is one of the issues the GUND Format was originally created to solve.

TEXT: BIOINFO INTERACTION SCORE per Second

DATA STORM OCCURENCE MAXIMUM: 4.89888 BACKFLOW: 187.69

WARNING: DATA STORM could damage GUND linker.

This graph is displayed when the reporter is speaking about the appearance of physical damage to GUND pilots emerging as a problem. It's difficult to tell exactly what this graph means, but I'll give my best deduction:

The graph is measuring the amount of interaction a pilot is currently having with a data storm, measured in seconds. The higher the Interaction Score, the greater a pilots exposure to the data storm. Thresholds of exposure are called "Stages" (as seen in the second image.) Based on the coloring, the higher the current stage of exposure, the more danger a pilot is in.

TEXT: WHAT ISSUE DO YOU WANT POLICY MAKERS TO SPEND TIME DISCUSSING?

(Left)

[Earthian Issue] Yes Poverty Reduction 95% Fair Trade 89% Educational Gap 89% Taxes 85% Employment 83% (Right)

[Spacian Issue] Yes Defense/Security 98% Free Competition 92% Infrastructure 90% Energy 87% Welfare 86%

I actually really really like this graph because of the stark difference between Earthian and Spacian issues. The issue of Gundams and defense doesn't even break the top 5 of what Earthians NEED policy makers to discuss. It's even more depressing when you realize the prologue is set 21 years before the main story, and not only have these problems not been addressed, they've actually gotten worse for the Earthians.

TEXT: HAPPY BIRTHDAY

It's Eri's BIrthday :3

There's zero way to deduce what the text on the whiteboard or the laptop in this picture could mean, but I really love this picture of Cardo and Elnora, so you should just look at it anyway.

TEXT: INSTALLATION COMPLETED C03_DISCONNECT TIMER

What this means is hard to pinpoint exactly, but presumably this person is working for Delling, and has uploaded a file into the main server of Folkvangr that will disconnect it from the network, so that there will be no way for anyone in the institute to call for help once the massacre begins.

TEXT: CONFIRM YOUR INTERNAL PMET SYSTEMS LINKED DEVICE AND PROGRAM FOR SUPPORTING SELECTION FOR CONTROL TEST

Just the screen that appears when Eri is linked to Lfrith. Presumably this screen appears for anyone who links to it.

TEXT: NO SIGNAL Code: CO4 CONNECTION IS LOST.

The Disconnect Timer we saw installed onto the Folkvangr server has just gone off.

TEXT: GUND FORMAT INTERCONNECT

ERICHT SAMAYA LAYER 34

The scene where Elnora sees that Ericht has not only gotten a callback from Layer 33, but has gone even further.

What I really like about this scene (and maybe I'm reading too much into it,) but look at the way the text is formatted on the screen. It's distinctly different than how it was when Elnora was trying to get a callback from Layer 33, specifically because, for some reason, it's displaying Eri's name. It didn't display Elnora's name earlier in the episode, and so the only way that makes sense is if, when Eri was talking to Lfrith and introduced herself by name,

It was listening.

(You can even see this during this shot. The display on screen is reacting to her voice)

Bonus: We can't see what the display on Nadim's Lfrith is saying when he goes permet score four cause he's currently having his brains melted out of his skull, but I'm gonna assume it says something along the lines of "You are currently having your brains melted out of your skull."

That's all for the prologue ! This will probably take me a long time to finish. But eh, I'll have fun with it.

Click here to move on to Episode 1! >>

Click here to go to the Masterpost!

[leedsomics]

moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks

CONCLUSIONS: Experimental results confirmed that moBRCA-net has a significantly enhanced performance compared with other methods, and the effectiveness of multi-omics integration and omics-level attention were identified. moBRCA-net is publicly available at https://github.com/cbi-bioinfo/moBRCA-net . http://dlvr.it/SnFzWp