#bioinformatic

[er-cryptid]

alright nerds, favorite biology (or biology-adjacent) field

had to make this new poll so there's more options

[felixcloud6288]

Seriously, genetics is weird.

I was reading one paper on long noncoding RNAs and there's this one part that just really stood out to me.

So to catch everyone up, genetic data is stored as DNA. Then parts of it go through a process called transcription to build a strand of RNA. Certain RNAs get translated into proteins, but there are noncoding RNAs that don't make proteins but instead do a secret second thing (and I mean secret cause there are tons of ncRNAs that no one knows what they do). long noncoding RNAs are just noticeably longer than average.

Anyway, one lncRNA mentioned in the paper is called WINCR1. When the researchers managed to block it from being used, they noted that cells lost the ability to divide and there was one particular gene GADD45B, which is responsible for triggering apoptosis, was more common in the cells.

So my guess is one of WINCR1's jobs is to just confirm to the self-destruct system that the DNA isn't broken. Like, it being transcribed essentially tells the cell that that part of the DNA is still working and it can then go and turn off the kill switch.

So I guess cells are just designed to kill themselves as their default setting and WINCR1 is the drinking bird pressing the Y key to tell the system to not just blow up.

[tired-coffee-addict]

I love autumn! 🍁

I'm getting interested in bioinformatics these days, but I'm not sure if i want to pursue it academically by master's degree or with a seminar. I started learning R coding this week by myself and it's going great, though it's too soon to determine if I enjoy it or not.

If anyone in bioinformatics stumbles on this post, comment what you like in your career and if you recommend it for someone interested in research!

[bacteriorage]

pinned post 👀

Hi! My name's Blue, and I'm studying for an integrated master's degree in biology at the University of Oxford. As my degree becomes less of a bachelor's and more of a master's, I wanted to share my experiences and use this blog as a record of my time here! Feel free to ask me anything about studying biology at Oxford or otherwise.

Interests:

Virology

Genomics

Epidemiology

Bioinformatics

Cell biology

Hobbies:

My main hobby in term-time is rowing. I also enjoy sewing, science fiction books, horror movies and caring for my pitcher plant Paula.

About me:

I am a former state comprehensive student who initially intended to go into something medicine-adjacent. I was pressured into applying for Oxford, but in hindsight I am very glad for that! Since then I have fallen in love with virology and bioinformatics. Also, my degree has become secondary to my burgeoning rowing career.

Feel free to drop me an ask any time!

[everythingaboutbiotech]

Summary of the 7 Habits of Highly Effective People by Stephen Covey. This book has had a profound impact on my life, and I hope it can help you too.

The 7 Habits are:🧵

Habit 1: Be Proactive

Don't be reactive to circumstances. Take responsibility for your life and the choices you make.

Focus on the things you can control, and let go of the things you can't.

Be proactive in your relationships and interactions with others.

Habit 2: Begin with the End in Mind

Have a clear vision for your life and what you want to achieve.

Break down your vision into smaller goals and steps.

Live each day in alignment with your vision.

Habit 3: Put First Things First

Distinguish between what is urgent and what is important.

Focus your time and energy on the things that are most important.

Learn to say no to things that are not a priority.

Habit 4: Think Win-Win

Look for ways to create mutually beneficial outcomes in your relationships and interactions.

Be willing to compromise and give and take.

Focus on the interests of others, not just your own.

Habit 5: Seek First to Understand, Then to Be Understood

Listen with the intent to understand, not just to reply.

Put yourself in the other person's shoes.

Be open to learning from others.

Habit 6: Synergize

Work together with others to create something greater than what you could achieve alone.

Appreciate the unique contributions of others.

Be open to new ideas and perspectives.

Habit 7: Sharpen the Saw

Take care of yourself physically, mentally, and emotionally.

Invest in your personal growth and development.

Be a lifelong learner.

I hope you found it helpful and inspiring.

Follow @everythingaboutbiotech for more inspiring stuff.

Remember, the 7 Habits are not a magic bullet. They take time and effort to implement, but they can be incredibly powerful tools for personal and professional growth.

[sr71blackbirdd]

Writing was my first love, my unconditional love perhaps, but STEM I had to try to love. STEM has equations and p-values and sitting at your computer all day trying to filter your 200 KB of data while you slowly lose your mind. Maybe I should have been a lit major or creative writing or something that I loved so naturally, but I love waking up every day and being able to call myself a scientist, not because it was easy money, but because it was hard to love.

[megumi-fm]

Hi Meg, I was wondering if I could get your insight on something... I'm interested in bioinformatics as a career but am not sure whether I should pursue just a Master's or try for a PhD. How did you decide how far you want to go with your education? I noticed you mentioned you hope to do a PhD someday? Thank you so much!

hey anon! okay, so in this answer I'ma focus on two things:

my thought process behind finalizing on a PhD

my approach to furthering education

I. Why PhD?

1. I love my subjects. I love the interdisciplinary nature of computational biology and it's sister subjects and I can see myself in academia- constantly learning and researching and exploring. 2. Even on the off chance that if I don't pursue a career in academia, I think I need a PhD anyway? Most high level positions in the industry for life-sciences requires a level of expertise that only comes with a doctorate, and I think my career opportunities (+ growth) will be rather limited without it.

Considering these two points, a PhD would be most suitable for me.

———————

Now, choosing the right type of graduate program can always be challenging because there are so many ways to go about it, and I am a very indecisive person so this was especially difficult for me. Here is my approach

II. Factors I considered before taking my next steps

My Primary Short-Term Goal(s)

I opted for a B.Tech in Biotechnology after 12th grade, and it is through the course of this degree that I realized my interest in computational biology and bioinformatics. My undergrad focused on too many topics and often emphasized wet lab over dry lab, so although I'm graduating with a specialization in Medicinal and Computational Biology, I don't know nearly enough regarding the computational aspects Thus, my short-term goal is to expand my theoretical understanding of the important aspects of bioinformatics & computational biology.

2. Course Options that Work

Now, I know that I want to continue my education, I've got two options- Masters and PhD. When I considered my immediate goal against these two options, I realized four things: a. I'm not equipped with the required dry lab skills to dive headfirst into research. b. I don't know enough bioinformatics to commit to anything long term right now c. I'm looking for a course that feels like an extension of my undergrad d. I want to keep my options open and consider all career opportunities Given these three options (+ course-related expenses + my skill level), it made most sense for me to choose a MSc at the moment rather than a PhD.

3. How the Course Ties in to My Long Term Goals

As I mentioned, my long term goal is to do a PhD. However, my upcoming graduate course is actually an MSc by Coursework degree, which- unlike a Thesis program, focuses on skill development (especially industry related) rather than research. In fact, most Thesis Masters can be converted to a PhD, but my program does not have that option. At first glance, this course might seem like it's going against my long term goal but consider: - Industry related or not, I need to develop computational skills before I can pursue research - After this course I might prefer to gain work experience for a couple years before opting for a PhD. - My preferred uni(s) for PhD are different from my preferred uni for Masters. [^To give an example on the last point, for masters i considered countries/unis known for their quality of education + closer to my home country (this will be my first time living abroad alone) but for my PhD, I'm looking at countries/unis that are pioneers in research for my subjects of interest (even if they are a lot farther away from home)] So essentially, I'm relying on this course to give me the skills and knowledge I need for a PhD in the future, while also giving me a buffer to understand and align my future goals and plans. Jumping from this to a PhD would be a lot harder than from a Thesis Masters, but that's a risk I'm willing to take.

So yeah, this was the way I went about choosing both my short term and long term academic goals. I hope this provides a good starting point for you! Don't stress out too much about it though; the truth is that there is no right or wrong choice, whatever decision you make will warp around your intentions and work for you the way you want it to. Best of luck for your future endeavors!!! I'm sure it'll all work out <3

[sparklingstudycare]

100 days productivity challenge

Day 4

Academics:

Immunology- 2 hours

Bioinfo- 1 hour

Course research- 40 mins

General:

Deeply cleaned the room

Arranged my stuff

Laundry

Journalling

@discountscholar @itsviiistudying @clipolscitrekkie

[biopractify]

Free online courses for bioinformatics beginners

🔬 Free Online Courses for Bioinformatics Beginners 🚀

Are you interested in bioinformatics but don’t know where to start? Whether you're from a biotechnology, biology, or computer science background, learning bioinformatics can open doors to exciting opportunities in genomics, drug discovery, and data science. And the best part? You can start for free!

Here’s a list of the best free online bioinformatics courses to kickstart your journey.

📌 1. Introduction to Bioinformatics – Coursera (University of Toronto)

📍 Platform: Coursera 🖥️ What You’ll Learn:

Basic biological data analysis

Algorithms used in genomics

Hands-on exercises with biological datasets

🎓 Why Take It? Ideal for beginners with a biology background looking to explore computational approaches.

📌 2. Bioinformatics for Beginners – Udemy (Free Course)

📍 Platform: Udemy 🖥️ What You’ll Learn:

Introduction to sequence analysis

Using BLAST for genomic comparisons

Basics of Python for bioinformatics

🎓 Why Take It? Short, beginner-friendly course with practical applications.

📌 3. EMBL-EBI Bioinformatics Training

📍 Platform: EMBL-EBI 🖥️ What You’ll Learn:

Genomic data handling

Transcriptomics and proteomics

Data visualization tools

🎓 Why Take It? High-quality training from one of the most reputable bioinformatics institutes in Europe.

📌 4. Introduction to Computational Biology – MIT OpenCourseWare

📍 Platform: MIT OCW 🖥️ What You’ll Learn:

Algorithms for DNA sequencing

Structural bioinformatics

Systems biology

🎓 Why Take It? A solid foundation for students interested in research-level computational biology.

📌 5. Bioinformatics Specialization – Coursera (UC San Diego)

📍 Platform: Coursera 🖥️ What You’ll Learn:

How bioinformatics algorithms work

Hands-on exercises in Python and Biopython

Real-world applications in genomics

🎓 Why Take It? A deep dive into computational tools, ideal for those wanting an in-depth understanding.

📌 6. Genomic Data Science – Harvard Online (edX) 🖥️ What You’ll Learn:

RNA sequencing and genome assembly

Data handling using R

Machine learning applications in genomics

🎓 Why Take It? Best for those interested in AI & big data applications in genomics.

📌 7. Bioinformatics Courses on BioPractify (100% Free)

📍 Platform: BioPractify 🖥️ What You’ll Learn:

Hands-on experience with real datasets

Python & R for bioinformatics

Molecular docking and drug discovery techniques

🎓 Why Take It? Learn from domain experts with real-world projects to enhance your skills.

🚀 Final Thoughts: Start Learning Today!

Bioinformatics is a game-changer in modern research and healthcare. Whether you're a biology student looking to upskill or a tech enthusiast diving into genomics, these free courses will give you a strong start.

📢 Which course are you excited to take? Let me know in the comments! 👇💬

[studentbyday]

30 days of intentionality

starting this challenge with the goal of taking it one day at a time. i have a hard time doing that these days. i spend more time ruminating on the past or worrying about the future than staying in the present, even if that's when i'm most content. not sure how i'll format my posts and most likely, i'll only do weekly updates bc daily ones are too overwhelming. i'll just go with the flow, trying to trust that everything will end up as it's meant to be and maybe i'll be more productive as focusing primarily on the present moment becomes a habit.

---

1. suo gân (arr. john williams for the ambrosian junior choir): i believe that if everyone lived by the idea of global citizenship and so saw the humanity in every individual from every background, there would be no war. reading the news fills me with fear, sorrow, and anxiety, but i also feel the responsibility to stay informed. did some studying today, more than yesterday, but it was kind of uncomfortable with the state of global politics lurking in the back of my mind. i'm still a little behind on school.

2. souvenir de paganini (chopin): today is not so bad. i'm making progress academically, but i do need to make time for social activities soon or i will get lonely and lose what little motivation i have very quickly.

3. once upon a december (arr. emile pandolfi): sometimes in the face of events and issues much bigger than myself that i have no control over, i feel like my dreams are pointless bc i think there's no way achieving them or trying to achieve them could possibly empower me to make real and important change that can truly benefit many. who knows if the future would even allow me to get that far. there are many things that could change the course of our lives that we don't have control over. but if others in worse situations than me and others much better informed than me can still have hope, then so can i. i didn't do much other than pharmacology and a little bit of philosophy today. i made more progress in pharmacology than expected, but that's only bc i didn't do any psych work. i also earned a few more mastery points on khan academy's integrated math 1 (not a priority, i know, but i wanted an easy win) and started lab tasks. i'm far from done with that, i need to do a little every day... i don't want to let them down! 🥺 (note to self: lying in bed is maybe NOT a good study break activity bc that just makes me not wanna do anything else after that and it's very very very hard to get out of that procrastination rut once i let myself fall into it.) 4. let's stay together (al green): everything should be going well, except i'm easily overwhelmed, and this time, it wasn't in an openly frazzled way, it was in a tired and slightly defeated "what's the point?" way, so i didn't realize it as quickly as i usually do. after some bed rest, cuddles 🧸, listening to steve jobs' commencement speech, and a little yoga, i felt better. "You can't connect the dots looking forward; you can only connect them looking backwards. So you have to trust that the dots will somehow connect in your future." was something i didn't know i needed to hear today. i modified my to-do list and found that the list of things i "must do" was nearly as long as the list of things i "want to do" 😅

5. kreutzer sonata, movt. 1 (beethoven): pretty sure i've mentioned some of these songs before but...they really fit the mood! sometimes i feel things so strongly that i develop a tightening in my chest that can only be relieved in a scream... since i can't actually scream and i don't actually really like the physical feeling of it, i scream through exercise and music 😅 beethoven is very nice for when i'm feeling very annoyed or angry, especially if it's an anxious kind of angry or if it's anger at injustice/inequality. i can't find a piano solo version that does the fiery spirit of the violin justice. so in the vague future when i actually play this, either i try (and perhaps fail) to replicate that on the piano, or i find a violinist friend who would want to play with me 😅 right now though, imagining how i would physically create that sound on the piano will have to be enough. the prevailing thought/feeling of the day: sometimes i just really wanna believe in the good in people and believe that i can trust (some of) them. i long for that feeling of safety in a broader irl community that i actually belong in. i'm surprised by how often i long for it. but then my negativity is reinforced by news and people's opinions on it.

6. violin sonata no. 1 in g minor, bwv 1001 (j.s. bach): stuff was done. i felt calm/chill throughout the day, but even tho i feel good whenever that happens, it usually means i don't get an extraordinary amount of things done that day (lol since when do i ever). i'm not sure if it's enough, as there is still lots to do and i'm pretty sure that it's just wishful thinking that i'll achieve all my goals for this week by its end. i need to cut down my goals list to the realistic rather than idealistic version as always (school, lab, and basic self-maintenance tasks) 😅 gaawwwdd i hope i can do this...good night.

7. waltz in a minor, b. 150 (chopin): today and yesterday i have been able to keep my phone time under an hour. the days are blissful (if not at least calmer) and focused. ����

8. only mine (laufey): cuddles in bed while listening to laufey is so soothing 🧸 takes me back to my childhood listening to lullabies in the dark 🥺 motivation to study is hard to find today. i just want to relax 🥺 i'll just do one tiny thing and see where i wanna go from there...

[felixcloud6288]

messenger RNAs are used to code proteins.

microRNAs(miRNA) block messenger RNAs from doing that.

Both are produced in the cell.

Every time I'm reading about miRNAs, I imagine a cartoon factory putting together a series of widgets along a complex conveyor belt that ends with it throwing the widget in an incinerator.

[gammaraydeath]

truthfully my birthday will be spent writing a 4 page essay about why my maximum likelihood tree failed to resolve a phylogeny and making a presentation for monday to go with it just so everybody in my class knows that i failed <3 but when i'm done i'm gonna get really drunk and play video games until i pass out and or die

[chialattea]

(Shrugs) I just think she’s neat

Rhea is @liliaceaae ‘s OC!!! Check out her page and find out more about Rhea because (holds her gently) she’s just a little guy,,,,

[febos]

Happy to share, ARTEMIS is now published at NAR!

https://doi.org/10.1093/nar/gkae758

ARTEMIS is a new tool for RNA/DNA 3D structure superposition and structure-based sequence alignment. Our benchmarks show that it outperforms the existing tools for both sequentially-ordered and topology-independent alignment.

ARTEMIS allowed us to identify an intriguing structural similarity between Lysine and M-box riboswitches (see the figure) and to describe the minor-groove/minor-groove helical packing motif. ARTEMIS is the first tool able to report several alternative superpositions, which makes it suitable for structural motif identification tasks.

ARTEMIS is available at GitHub: https://github.com/david-bogdan-r/ARTEMIS

Thanks to Davyd Bohdan, Janusz Bujnicki, & International Institute of Molecular and Cell Biology in Warsaw!

[historyofsky]

Sooo I’m 24 but never joined tumblr. Idk why. But I recently discovered a YouTube Chanel with video essays about tumblr history and was intrigued. I had to do it.

And I heard that you shouldn’t join now. But I like to make mistakes so here am I. And I need help. How do I use this? I feel so old. How do I find my ppl? Am I embarrassing myself? (Probably yes but ew) what are the social norms on here? Can someone adopt a newbie?

#help I guess?

Ps just discovered tags hihi ✨

[philosophiesde]

Zoomposium with Dr. Gabriele Scheler: “The language of the brain - or how AI can learn from biological language models”

In another very exciting interview from our Zoomposium themed blog “#Artificial #intelligence and its consequences”, Axel and I talk this time to the German computer scientist, AI researcher and neuroscientist Gabriele Scheler, who has been living and researching in the USA for some time. She is co-founder and research director at the #Carl #Correns #Foundation for Mathematical Biology in San José, USA, which was named after her famous German ancestor Carl Correns. Her research there includes #epigenetic #influences using #computational #neuroscience in the form of #mathematical #modeling and #theoretical #analysis of #empirical #data as #simulations. Gabriele contacted me because she had come across our Zoomposium interview “How do machines think? with #Konrad #Kording and wanted to conduct an interview with us based on her own expertise. Of course, I was immediately enthusiastic about this idea, as the topic of “#thinking vs. #language” had been “hanging in the air” for some time and had also led to my essay “Realists vs. nominalists - or the old dualism ‘thinking vs. language’” (https://philosophies.de/index.php/2024/07/02/realisten-vs-nominalisten/).

In addition, we often talked to #AI #researchers in our Zoomposium about the extent to which the development of “#Large #Language #Models (#LLM)”, such as #ChatGPT, does not also say something about the formation and use of language in the human #brain. In other words, it is actually about the old question of whether we can think without #language or whether #cognitive #performance is only made possible by the formation and use of language. Interestingly, this question is being driven forward by #AI #research and #computational #neuroscience. Here, too, a gradual “#paradigm #shift” is emerging, moving away from the purely information-technological, mechanistic, purely data-driven “#big #data” concept of #LLMs towards increasingly information-biological, polycontextural, structure-driven “#artificial #neural #networks (#ANN)” concepts. This is exactly what I had already tried to describe in my earlier essay “The system needs new structures” (https://philosophies.de/index.php/2021/08/14/das-system-braucht-neue-strukturen/).

So it was all the more obvious that we should talk to Gabriele, a proven expert in the fields of #bioinformatics, #computational #linguistics and #computational #neuroscience, in order to clarify such questions. As she comes from both fields (linguistics and neuroscience), she was able to answer our questions in our joint interview. More at: https://philosophies.de/index.php/2024/11/18/sprache-des-gehirns/

or: https://youtu.be/forOGk8k0W8