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@Biologyandbiotechnology-qc5jo 6 күн бұрын
good expression
@Harshal378 24 күн бұрын
I had a question. Can I use the confidence score to generate a weighted centrality network? If yes, can anyone give me some answer, on how to upload the information to the exported network.
@larsjuhljensen 22 күн бұрын
I’m not sure I understand your question correctly. If you ask if you can calculate e.g. weighted degree centrality by summing the confidence scores, the answer is yes.
@Harshal378 21 күн бұрын
@@larsjuhljensen I am sorry, I should have explained it better. I was asking whether we have a plugin on cytoscape which can use these confidence scores to give us weighted centrality networks. I have used CytoNCA, but I couldn't upload the scores to give me a proper network.
@larsjuhljensen 20 күн бұрын
I managed to get CytoNCA to work. The trick is that for weighted networks, it requires a column called “weight” in the edge table. So if you create a column with that name and copy the stringdb::score column into it, you will get the desired result. It would obviously be a lot more elegant if CytoNCA allowed you to specify which column contains the weights instead of relying on a fixed column name, but it doesn’t.
@larsjuhljensen 27 күн бұрын
AnythingLLM is an easy-to-install open-source document chatbot with a graphical user interface, which allows you to upload documents, import a GitHub repository, import a KZbin transcript, or scrape a website. Once the documents have been loaded, they will be indexed in a vector database and you can chat with the documents using any large language model (LLM), including ChatGPT and locally hosted LLMs downloaded from Hugging Face. Being able to use an open source and open models to run a fully local document chatbot his highly attractive from a data privacy and security perspective.
@CatarinaCosta-rt3wj Ай бұрын
Great videos! Thank you for sharing them with us! I have a quick question - When we provide as input multiple proteins, the first image we get is all the input proteins connected (or not) by either evidence or confidence. My question is - the localization of each protein in this image has some kind of meaning or is it random? I was wondering if perhaps it would mean that some proteins may be closer to each other because they share some specific features even if they are not connected by evidence/confidence. Thank you!
@larsjuhljensen Ай бұрын
You're welcome! The short answer to your question is that the position does not mean anything. It is not random - it is generated by a layout algorithm. I have a short video on the topic: kzbin.infoF3Nrqjxlw4A?feature=share
@larsjuhljensen Ай бұрын
For more information and to register for the meeting see: eventsignup.ku.dk/8danishbioinfconference
@TommyCarstensen Ай бұрын
Unfortunately I missed the registration deadline for this. Have fun everyone.
@larsjuhljensen 27 күн бұрын
You can still register for the symposium on the last day, though! conferencemanager.events/2ndsymposiumonapplieddeeplearninginbioinformatics
@ashokprabhu8036 Ай бұрын
I learnt String/Cytoscape looking at your videos. This one was special! Thank you very much sir.
@larsjuhljensen Ай бұрын
Wonderful to hear, thank you!
@vicjndarigfan 2 ай бұрын
Hello, I have been struggling to get positional information or subcellular localization of proteins as demonstrated in 4:44 using Cytoscape String. Can you please provide links/explanations for this?
@larsjuhljensen Ай бұрын
Which organism are you working on? We only have subcellular localization information for a subset of the organisms in STRING.
@sirishasunkara7086 2 ай бұрын
Is there an opportunity to participate virtually? Unfortunately, travel budgets are tight, and a few of my colleagues and I may be able to make it to a virtual conference. Thank You!
@larsjuhljensen 2 ай бұрын
The registration says that it's an in-person conference, so I don't think there will be an online option.
@sirishasunkara7086 2 ай бұрын
@@larsjuhljensen Ugh - that is so unfortunate for so many of us... Thanks for the message.
@larsjuhljensen 2 ай бұрын
For more information, proposal submission, and registration see scverse.org/conference2024/
@slendrmusic 2 ай бұрын
Thanks
@larsjuhljensen 27 күн бұрын
You're welcome!
@gabnaressi 2 ай бұрын
Amazing overview of techniques, thank you!
@larsjuhljensen 2 ай бұрын
Glad you enjoyed it!
@Arurukshu 2 ай бұрын
How to use cytoscape for nutrigenomics. I want to understand links of wheat with proteins, metabolic pathways and diseases. Please guide me sir
@larsjuhljensen 2 ай бұрын
What would be the data that you want to start from? Is it wheat or human proteins you want in the network?
@Arurukshu 2 ай бұрын
@@larsjuhljensen i want to analyse wheat. i have another question sir, how i can analyse my compound's effect on polymorphic genes using cytoscape? please guide me sir. i know how to assess on disease genes. but want to know how to assess effect on polymorphic genes.
@Arurukshu 2 ай бұрын
Hello sir...i want to use cytoscape for nutrigenomics. To analyse effect food on genes and pathways. I did get where to start. Previously i did network analysis for phytochemicals. But for foods especially with potassium calcium etc their effect, how to create network. Please guide me
@adeniyitbabz5845 2 ай бұрын
Thanks for the advice👍
@larsjuhljensen 2 ай бұрын
No problem 👍
@smilefaxxe2557 2 ай бұрын
great video!
@larsjuhljensen 2 ай бұрын
Thanks!
@SyedTauheed-xg6pc 2 ай бұрын
Fantastic videos so far Lars, you have done the world a service.
@larsjuhljensen 2 ай бұрын
Thanks for the kind words!
@slendrmusic 2 ай бұрын
5:08 one of the most useful diagrams I've seen in a while
@larsjuhljensen 2 ай бұрын
Thank you!
@techyunited9086 3 ай бұрын
Hello Professor, for the enrichment analysis from a cluster generated from an unclustered network by mcl clustering, can I use the genome as the background instead of the unclustered network?
@larsjuhljensen 3 ай бұрын
You can but the results would be different. If you use the whole genome as a background, you may find some terms that are overrepresented in almost all clusters, because they are simply enriched in the network in general. That's why I prefer to do two separate enrichment analyses: one that compares the whole network vs. the genome to find out what is generally overrepresented, and another that compares each cluster to the network to find out what is special about each cluster.
@techyunited9086 3 ай бұрын
Thank you for the reply
@larsjuhljensen 3 ай бұрын
The Seshat AI extension for text-generation-webui can be found here: github.com/larsjuhljensen/Seshat
@tiamat1628 3 ай бұрын
Awesome smart stuff
@science_mbg 3 ай бұрын
Thanks for the short and detailed video. I have one question: Are you using Nvidia eye contact ON (eye stabilization)? Otherwise, it feels a bit different.
@larsjuhljensen 3 ай бұрын
No, I did try it a while back. I found it to give some strange artifacts that I really didn't like. Are you suggesting that it's worth trying out again?
@zackhades641 3 ай бұрын
Really really appreciate you walking through the steps (at a perfect pace)! Subscribed!
@larsjuhljensen 3 ай бұрын
Thanks for the sub!
@larsjuhljensen 3 ай бұрын
More info and registration:: conferencemanager.events/2024-summerschoolonapplieddeeplearninginbioinformatics
@Alexeco13 3 ай бұрын
Hi, I would like to know what is the minimum level of skill needed in programming to be there. Thanks!
@larsjuhljensen 3 ай бұрын
@@Alexeco13 Expect all exercises to take place in Jupyter notebooks, so some familiarity with Python is needed. But this is not a course where you'll need to code up anything from scratch.
@Alexeco13 3 ай бұрын
Perfect! Thanks!!
@michealogar7255 3 ай бұрын
Will Virtual attendance be allowed?
@larsjuhljensen 3 ай бұрын
I don't think so. The course is very much a hands-on course, so running it in a mixed physical and virtual setup would be a nightmare.
@vagpafilis 4 ай бұрын
Lol nice
@WooShell 4 ай бұрын
Unfortunately, this is where the scientific writing will be heading in the near future.. already tons of useless GPT generated papers are published every day.
@muungani 4 ай бұрын
Lol 😂
@keerthana7353 4 ай бұрын
You summarised my entire semester of listening to droning lectures. I don't know why we don't have more effective teaching in schools. THIS WAS SO MUCH BETTER.
@larsjuhljensen 4 ай бұрын
Thanks, that comment made my day! Sorry that you had to sit through those lectures, though. We've all been there and carry the scars 😉
@kajalpanchal8239 4 ай бұрын
hey! this is a great overeview, cn you share proper refeerences
@larsjuhljensen 4 ай бұрын
Aside from the references to where figures are from, I unfortunately do not have them. This overview was simply based on what I know - I do not know where I know each thing from, and digging up references for it would be equivalent to doing the work for writing a review article on the topic.
@sethujaganathan 4 ай бұрын
Thank you sir for all your efforts! Appreciate it!
@larsjuhljensen 4 ай бұрын
You're very welcome - I enjoy making them!
@virgirma1328_PhD_scholar 4 ай бұрын
Good morning teacher.Thanks for the educative content. Could you please indicate which version of Cytoscape you are using for the above tutorial?
@larsjuhljensen 4 ай бұрын
It was probably Cytoscape 3.9.x given when it was recorded, but not much should have changed to the current 3.10.x version.
@larsjuhljensen 5 ай бұрын
Link to the "Ask STRING" assistant: hf.co/chat/assistant/65e456ff665eb29b9e87c95b
@laurencebindschedler-spanu5747 5 ай бұрын
Lovely 10 min course, a great introduction for students!
@larsjuhljensen 5 ай бұрын
Thank you - it was a tough topic to try to cover in a short format!
@logitfau252 5 ай бұрын
great project! Iam doing a systematic review right now and its really handy, but not working for me somehow. when creating database whole page just becomes greyish
@larsjuhljensen 5 ай бұрын
Try contacting the developers in Athens - since it is running on their server, I'm unable to help you find out what is going wrong.
@logitfau252 5 ай бұрын
@@larsjuhljensenthat was a quick answer! Thank you alot :)
@augustop3631 5 ай бұрын
Great talk! Thank you very much for sharing. Is FAVA already implemented on Cytoscape STRINGapp v12? For example if I do network clustering based on string::coexpression? I always wondered how to better use clustering for discovering new and interesting protein associatons on DEGs/DAPs of omics considering that the clustering was made only on known associations.
@larsjuhljensen 5 ай бұрын
Yes, FAVA is the co-expression channel of STRING as of v12. And if you get networks in Cytoscape stringApp, they are from the latest version if STRING, i.e. currently form v12.
@augustop3631 5 ай бұрын
Thank you! That is great
@kiterunner29 5 ай бұрын
Great post.
@larsjuhljensen 5 ай бұрын
Thank you, glad you enjoyed it :-)
@larsjuhljensen 5 ай бұрын
sciencecluster.dk/event/cross-cluster-collaboration-data-science-for-planetary-and-human-health/
@washingtonwuyi9534 5 ай бұрын
thank you, you're a good man.😘
@larsjuhljensen 27 күн бұрын
You're welcome, I hope it's useful for people.
@settembrini42 5 ай бұрын
You are the best!
@KonstantinE-tt5bi 5 ай бұрын
😂 well done. Looking forward to roast my bachelors thesis
@larsjuhljensen 5 ай бұрын
UnderwheLLM is a humorous take on the notorious "reviewer 2" who will write a ruthless negative report that destroys manuscript, often after seemingly only skimming it. Such reviewers are hopefully getting ready for retirement, and they can easily be replaced by AI. Using the Mixtral 8x7B and a short system prompt with instructions, I have created the UnderwheLLM assistant, which you can find at underwhellm.jensenlab.org (hosted by HuggingChat). Try it by pasting in the title and abstract of your own manuscript to prepare for the future, your competitor's paper to feel better, or a famous paper for a cheap laugh. But please do not use it to review any actual manuscripts!
@blago7daren 5 ай бұрын
Big thanks!
@larsjuhljensen 5 ай бұрын
You're welcome!
@muhammadwaqasluqman2977 5 ай бұрын
wow, thank you so much.
@larsjuhljensen 5 ай бұрын
You're welcome, I hope this short overview was useful!
@ghizlane3124 5 ай бұрын
Thank you
@RCQazi 6 ай бұрын
Indeed an inspiration for many young bioinformaticians out there, including me.
@larsjuhljensen 5 ай бұрын
Thank you!
@sara_rojo 6 ай бұрын
I watched several videos trying to find an easy explanation about this. You made it so simple. Thank you. Best regards from México:)
@larsjuhljensen 5 ай бұрын
Glad it was helpful!
@xinglinjiang4952 6 ай бұрын
but do not all proteins evolved from one single ancestor? like all animals come from a single single cell ancestor?
@larsjuhljensen 5 ай бұрын
While gene duplication is the most common mechanism leading to the creation of new protein-coding genes, it is not the only. New protein-coding genes can also evolve from non-coding regions in DNA (see e.g. www.pnas.org/doi/full/10.1073/pnas.0509809103). All proteins are thus not derived from a single ancestral open reading frame.
@user-qv1ci6qg6y 6 ай бұрын
Wow, great explanation. This has given me a general insight into Mass spectrometry.
@larsjuhljensen 6 ай бұрын
Thank you! I'm always happy when people find my videos useful :-)
@mongolitosking9739 6 ай бұрын
Does the multiplex approach that you mentioned refers to the SWATH method ?
@larsjuhljensen 6 ай бұрын
I was not thinking of SWATH, although SWATH is compatible with multiplexing (as far as I know). What I had in mind was labeling approaches such as iTRAQ and TMT, which allow you to multiplex 8 and 16 samples respectively.
@biruk8617 6 ай бұрын
This is a very great introduction for beginners in HRMS. Thank you.
@larsjuhljensen 6 ай бұрын
You are very welcome, I'm glad you liked it!