Starred posts | chat.stackexchange.com

Martin Sleziak

Aug 24, 2022 13:49

2

Q: Announcing a “Graduation” election for 2022

Summary: Bioinformatics Stack Exchange will begin the nomination stage for an election on September 19th, 2022, as your “graduation” election! The timeline: On September 12, 2022, I'll post a question collection post on Meta, so that the community can post questions they'd like to see the candid...

2

Geraldine_VdAuwera

Apr 24, 2020 16:41

Hi everyone, just wanted to introduce myself since I plan to be fairly active on here going forward. I'm responsible for outreach for the Data Sciences Platform at the Broad Institute (which makes GATK etc) and am also a core member of the OpenWDL workflow development community.

4

M__

Jun 2, 2023 14:26

This looks good. However, because I no longer use institutional clusters, I will not be able to verify the information, but I will try and cool. I use cloud computing. Cloud computing is on balance more powerful (and cheaper for GCP), thats why, but it depends on the institute. If it's subsidised by the institute then cost/power changes. Thanks. I'll hopefully return with wiki details (lets see).
BTW please do star one of my chat posts here (like this one) - its good site sites :-)

Indira

Jun 2, 2023 14:23

I can draft it out with you if it helps as I have to keep using Singularity for multiple programs

Ram RS

May 31, 2023 14:42

@M__ No, my point is that the HPC architecture (or absence of it) does not matter at all. singularity runs on the computer you run the command on. Once inside singularity shell, they should not be able to see other file systems unless there is some sort of automount being triggered at the wrong moment here. As far as I can see, singularity only binds $HOME by default, launching a shell with $HOME as $PWD.

Indira

May 30, 2023 15:55

I just saw your comment now?

Kirti Kulanthaivel

May 24, 2023 16:03

Thank you M__, was a pleasure talking to you

Kirti Kulanthaivel

May 24, 2023 15:40

Okay.. I thought Iqtree did that for me

M__

May 24, 2023 15:40

iqtree generates a treefile and it will comprise bootstrap values

Kirti Kulanthaivel

May 24, 2023 15:39

@M__ change the option in branch lengths? that's in FigTree?

M__

May 24, 2023 15:38

okay ... to summarise:
* please check if trimal needs an amino acid flag
* -T 4 is good when no one is using the machine
* manually checking the alignment is a good idea e.g. seqotron (might be too big), they'll be a genomic equivalent
* take the output suffixed by 'treefile' and load it in FigTree'
* the bootstraps will not automatrically appear you have to change an opition in 'branch lengths'

Kirti Kulanthaivel

May 24, 2023 15:37

If you don't mind me asking you, you a professor? How do you know so much.. if you don't want to answer just pass.. thank you so much.. it's difficult to get help around even if ppl know the answer

M__

May 24, 2023 15:36

-m JTTDCMut + G -T 4 -B 100

Kirti Kulanthaivel

May 24, 2023 15:35

-m JTTDCMut + G -T 4

Kirti Kulanthaivel

May 24, 2023 15:34

how to use JTTDCMut?

M__

May 24, 2023 15:30

it is very hard to parallelise a maximum likelihood, but parallelising bootstrapping is easy

llrs

Dec 21, 2021 08:30

The site lost the beta status: meta.stackexchange.com/questions/374096/…!!

2

Laura

Feb 27, 2023 15:21

Thank YOU!

Laura

Feb 27, 2023 15:13

Thank you. I'll keep that in mind. In the case you last described though, it means that I can't use sequence similarity in 'everything else'? Because if one point is sequence 'A', there would be some value for its loops (coordinate:x), and for y it would be sequence simiarity to...what? B? C?...Z? Which does not mean it's a bad idea by any means - it simply doesn't solve my problem right now xD

Laura

Feb 27, 2023 15:13

I'll accept the original answer as being close enough to what I imagined (and for explaining that some things just don't work and why), but I may end up just trying to figure out some Python code to better sort my 16S rRNA Excel ANI matrix for easy viewing (which is not publishable, but it helps). Thank you!

Laura

Feb 27, 2023 15:01

ANI (Average nucleotide identity) for genomes, in the case of that figure, but would be the same for genes. I don't necessarily need to add the tree - the tree would be its own separate thing - but I guess this type of figure wouldn't work for hundreds of sequences any better than my Excel matrix does.

Laura

Feb 27, 2023 15:01

And, I don't need the thing to be publishable, just for some way to better get an idea of 'this group of strains is closely related/these two groups aren't that closely related even though they group together in the tree'. I thought that a PCA-like image might be more elegant than my Excel sheet, and that it would work since it shows similarity (in a way), but apparently that's not quite the case....

Laura

Feb 27, 2023 15:01

I use some loops in my work (D1-D1',BoxB), but not all sequences have them. Whereas all sequences have, by default, some sequence similarity to another homologous sequence.

Laura

Feb 27, 2023 14:50

Like this mdpi.com/genes/genes-12-00071/article_deploy/html/images/…?

Laura

Feb 27, 2023 14:48

I'm trying to follow. So basically it means that it won't work if I want each dot to be a sequence (and the distance between dots corresponding to sequence similarity, the higher the sequence similarity the closer the dots, it won't work, because sequence similarity is not the property of one dot (sequence), it's the property of any two dots (sequences)?

terdon

Nov 12, 2022 19:16

@NickODell I would argue that means the question is off topic as it is no longer a programming question but is now a plink question.

terdon

Nov 12, 2022 18:07

Is there any point in having this tag for SO? Sure, parsing the output of plink-genomics can be hard, but that's just a text processing task. So you can tag with a general text-processing and perhaps also a general bioinformatics tag, so you can just delete the plink-genomics tag and be done with it. Is that not simpler and more appropriate for SO? — terdon 20 secs ago

Martin Sleziak

Sep 18, 2022 06:12

4

Q: 2022 Moderator Election Q&A – Question Collection

Bioinformatics Stack Exchange is scheduled for an election next week, 2022-09-19. In connection with that, we will be holding a Q&A with the candidates. This will be an opportunity for members of the community to pose questions to the candidates on the topic of moderation. Participation is compl...

discussion featured election

Feeds

Aug 14, 2020 06:21

Devon Ryan has unfrozen this room.

2

Martin Sleziak

May 18, 2022 10:42

166

Q: Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... 1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct 61 gttctctaaa cgaactttaa aatctgtgtg gctgtcactc ggctgcatgc ttagtgcact 121 cacgcagtat aattaataac taattactgt cgttgacagg a...

sequence-alignment fasta phylogenetics sequencing covid-19

terdon

May 18, 2017 14:23

Biostars and Seqanswers are the best available bioinformatics Q&As but they're crap compared to the SE system.

4

terdon

Apr 6, 2022 17:29

By the way, @M__, we're also looking in the UK. If you, or anyone you know, is interested, see docs.google.com/document/d/…

terdon

Apr 6, 2022 16:10

14

A: Receiving Stack Overflow's Chat Notification

There are several ways to receive notifications from chat. If the chat window is not focused when a message would ping you then a notification will show up in your inbox within roughly 15 minutes. Otherwise, a message will ping you if you are currently in the room. Triggering a ping in chat c...

Kamil S Jaron

Apr 18, 2018 13:45

We got more than 1000 questions. Good job everyone.

3

Kamil S Jaron

Jan 9, 2022 14:29

@llrs Yaaaay

Kamil S Jaron

Dec 20, 2021 19:26

@user1271772 That's a strange question. I would say the premise should not be generalized to "bioinformatics" because loads of bioinfo papers describe abstract structures / data types / algorithms without proving experimentally their utility. The same applies to popgen, there are even fully theoretical journals out there that publishing nothing else then theory. However, I am not much structural biology person, can't really speak about what happen there....

user1271772

Dec 20, 2021 00:49

8

Q: Why are condensed matter predictions considered on par with experiment, while structural biology modeling receives more skepticism?

I have two main modeling research lines: one related to structural biology (including rational drug design, de novo design, polymorphism, etc.) and the other one related to condensed matter (nanostructures, crystals, etc.). Any time I submit a manuscript in the biological area, either the editors...

density-functional-theory condensed-matter nanostructures publishing structural-biology

Nike Dattani

Mar 30, 2021 16:34

5

Q: What software is the best choice for RNA structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. What can be said about RNA structure prediction? Are there promising advancements? For me, it has relevance in connection with the origin of life (cf. RNA world). I have only heard about the ViennaRNA Package, and there is...

software software-recommendations structural-biology

jakebeal

Feb 22, 2021 22:00

The Synthetic Biology Area51 proposal is now in the commitment phase. Most of the community coming in are from outside of StackExchange, so we particularly want to invite experienced StackExchange folks to commit and be able to help show the newly-arriving experts the ropes!
If you have any interest in this area, please come and commit!
https://area51.stackexchange.com/proposals/125068/synthetic-biology?referrer=YjdhY2I1OGNlNjVmOWVhNTIyOWVmMDZiM2JiMDZkMmY5YTc0NDExNzU1ZWQ5MTIzMGJlMTAyNzFlNzM2MjY3YwDW6Nx4qgOvu3rvs7-1xHvcB0c8LQ8UvjuUpWWiAnAO0

Nike Dattani

Dec 7, 2020 00:59

2

Q: Can AlphaFold predict protein structures around metals well?

(1) Commonly, the metal is at the active site which needs the most prediction precision. (2) Typically, there is only one (or a few) metals in a protein, which contains far more other atoms. So, the structural data that could be used to train AlphaFold could contain far less information about the...

transition-metals proteins machine-learning metal-complexes protein-folding

Martin Sleziak

Oct 2, 2020 04:20

3

Q: Should something be done about frozen "main" chatroom?

I have noticed that the "main" chatroom for this site has been frozen. By the main chatroom I mean the room which was created when the site was created with the description "General discussion for bioinformatics.stackexchange.com". As far as I know, the Stack Exchange chat system will still keep ...

discussion chat

Martin Sleziak

Oct 2, 2020 04:20

0

A: Should something be done about frozen "main" chatroom?

I think its a resource for the site, not that I've used it much, but I think I should have used it rather than create new 'chat rooms'. I think we just need to be mindful of posting a random 'chat' into the room to keep it afloat. Its a bit like the Parsees keeping their ceremonial fire alight f...

Nike Dattani

Sep 20, 2020 18:50

8

Q: Computational biology textbook similar to "Computational Materials Science" by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD simulations and also uses examples with code from LAMMPS. I was wondering if there are any MD related texts...

molecular-dynamics reference-request molecular-modeling gromacs

Timur Shtatland

Sep 11, 2020 20:55

What should be the name for the new [*vcf*] tag related to bioinformatics vcf file format? - Meta Stack Overflow
https://meta.stackoverflow.com/q/401119/

Vass

Sep 5, 2020 02:12

Hello everyone. Just here to say hi and that I am excited to be doing bioinformatics again after literally 10years! It feels strange but familiar at the same time. A lot seems to have changed with tons of progress. Working on getting up to speed again.

terdon

Jun 13, 2017 13:46

I can understand being more lenient during this first phase, but if we get used to not downvoting for fear of appearing "mean" we end up with yahoo answers.

2

kenorb

Jun 1, 2017 11:13

Upvote this post on reddit please, so we can have more people to join.

2

Kusalananda

May 31, 2017 17:15

Hi people. After having @terdon point out the site to me yesterday, I joined. I also set around a link to people at work, and at least one colleague signed up. One of the managers were also very enthusiastic. I'll make a new push tomorrow.

2

Tensibai

May 16, 2017 18:26

I know, but I'd prefer to let you committed users take the dance of private beta first :)

2

skullpatrol

Mar 28, 2020 03:22

.