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SIB - Swiss Institute of Bioinformatics
Швейцария
Добавлен 23 ноя 2014
The SIB Swiss Institute of Bioinformatics is an internationally recognized non-profit organization dedicated to biological and biomedical data science. Its data scientists are passionate about solving complex questions in many fields, from biodiversity and evolution to medicine, and offer their expertise and services to academic, clinical, and industry groups.
SIB federates the Swiss bioinformatics community of some 800 scientists, encouraging collaboration and knowledge sharing.
The Institute contributes to keeping Switzerland at the forefront of innovation by fostering progress in biological research and enhancing health.
Data scientists for life
www.sib.swiss
If you are a SIB Member and wish to upload a video on the channel, please contact the SIB Communications Department.
SIB federates the Swiss bioinformatics community of some 800 scientists, encouraging collaboration and knowledge sharing.
The Institute contributes to keeping Switzerland at the forefront of innovation by fostering progress in biological research and enhancing health.
Data scientists for life
www.sib.swiss
If you are a SIB Member and wish to upload a video on the channel, please contact the SIB Communications Department.
Enzymes: Extracting Biological Insight Using UniProt
UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information. Enhanced enzyme annotation in UniProtKB is based on Rhea, a comprehensive expert-curated database of biochemical reactions that uses the ChEBI ontology to describe reaction participants.
Starting with a biological question (I.e., Could you refine my list of enzymes to identify the ones with cysteine at the active and/or allosteric sites?), you will explore the different ways of answering it, using UniProt's advanced query, or SPARQL when the use of UniProt advanced queries is not applicable. Hints on how to extend queries to other biological contexts w...
Starting with a biological question (I.e., Could you refine my list of enzymes to identify the ones with cysteine at the active and/or allosteric sites?), you will explore the different ways of answering it, using UniProt's advanced query, or SPARQL when the use of UniProt advanced queries is not applicable. Hints on how to extend queries to other biological contexts w...
Просмотров: 193
Видео
Detecting inbreeding depression in structured populations
Просмотров 163Месяц назад
What you will discover: a mixed model with an allele-sharing-based relatedness matrix to estimate more efficiently inbreeding depression in structured populations. You are: a biologist or bioinformatician who needs to estimate the inbreeding depression in a group of related individuals Speaker: Eléonore Lavanchy, a member in Jérôme Goudet’s group based in Unil in Lausanne. Click to access speci...
GeneSelectR: how to identify relevant features in RNA sequencing datasets
Просмотров 3013 месяца назад
What you will discover: GeneSelectR, an open-source R package that innovatively combines ML and bioinformatic data mining approaches for enhanced feature selection during High-dimensional Bulk RNA sequencing. You are: a bioinformatician who performs bulk RNAseq analysis but struggles with batch effects Speaker: Damir Zhakparov, a PhD candidate in Katja Baerenfaller’s group based in Swiss Instit...
Wilhelm Dirks - Cell lines in the 21st century symposium
Просмотров 814 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Tadashi Kondo - Cell lines in the 21st century symposium
Просмотров 334 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Niels C. Bols - Cell lines in the 21st century symposium
Просмотров 454 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Jan van der Valk - Cell lines in the 21st century symposium
Просмотров 404 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Florian M. Wurm - Cell lines in the 21st century symposium
Просмотров 564 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Anita Bandrowski - Cell lines in the 21st century symposium
Просмотров 314 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Amos Bairoch - Cell lines in the 21st century symposium
Просмотров 384 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Andreas Kurtz - Cell lines in the 21st century symposium
Просмотров 404 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Amanda Capes Davis - Cell lines in the 21st century symposium
Просмотров 804 месяца назад
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
CellCharter: flexible and scalable spatial cell niches
Просмотров 1464 месяца назад
What you will discover: CellCharter is a computational framework designed to uncover and analyze communities of cells within tissues. Its primary goal is to reveal how distinct types of cell band together and function in targeted areas. In this video, you will also see how you can use CellCharter to detect artifacts from immunofluorescence data. You are: a cancer biologist, developmental biolog...
An Introduction to Nextflow and nf-core
Просмотров 3634 месяца назад
This talk was recorded live during the SIB course “ Reproducible Research and Data Analysis using Nextflow Pipelines” (www.sib.swiss/training/course/20211115_NEXTF) which took place online on 15-18 November 2021. The course material can be found on the dedicated course GitHub repository (github.com/biocorecrg/SIB_course_nextflow_Nov_2021?tab=readme-ov-file) and course GitHub Page (biocorecrg.gi...
Easy simulation of species trees and populations over time using ReMASTER
Просмотров 814 месяца назад
What you will discover: ReMASTER, a phylodynamic simulation tool designed for BEAST 2 to analyze molecular sequences. You are: an evolutionary biologist, epidemiologist - or generally interested in phylodynamic simulations, then this talk is for you! Speaker: Tim Vaughan, Senior Scientist at Computational Evolution led by Tanja Stadler. Click to access specific sections of the talk: - 00:53 Lea...
How to boost your research with SIB’s Semantic Web of data
Просмотров 2555 месяцев назад
How to boost your research with SIB’s Semantic Web of data
prolfqua: A comprehensive R package for protein differential expression analysis
Просмотров 8428 месяцев назад
prolfqua: A comprehensive R package for protein differential expression analysis
Reading tabulated data with pandas (1 of 9)
Просмотров 1529 месяцев назад
Reading tabulated data with pandas (1 of 9)
Data manipulation: selecting rows and columns (2 of 9)
Просмотров 729 месяцев назад
Data manipulation: selecting rows and columns (2 of 9)
Data Analysis and Representation in Python - DataFrame subsetting (3 of 9)
Просмотров 569 месяцев назад
Data Analysis and Representation in Python - DataFrame subsetting (3 of 9)
Data Analysis and Representation in Python - Operations on columns (4 of 9)
Просмотров 389 месяцев назад
Data Analysis and Representation in Python - Operations on columns (4 of 9)
Data Analysis and Representation in Python - Deleting and adding rows, and writing to file (5 of 9)
Просмотров 399 месяцев назад
Data Analysis and Representation in Python - Deleting and adding rows, and writing to file (5 of 9)
Data Analysis and Representation in Python - Basic description, common summary statistics (6 of 9)
Просмотров 909 месяцев назад
Data Analysis and Representation in Python - Basic description, common summary statistics (6 of 9)
Data Analysis and Representation in Python - Basic representation: plotting one column (7 of 9)
Просмотров 449 месяцев назад
Data Analysis and Representation in Python - Basic representation: plotting one column (7 of 9)
Data Analysis and Representation in Python - Accounting for categories in the data (8 of 9)
Просмотров 529 месяцев назад
Data Analysis and Representation in Python - Accounting for categories in the data (8 of 9)
Data Analysis and Representation in Python - scatter/line plots, exporting, and conclusion (9 of 9)
Просмотров 579 месяцев назад
Data Analysis and Representation in Python - scatter/line plots, exporting, and conclusion (9 of 9)
Optimizing Python Code for Better Performance - Timing objects in python (1 of 8)
Просмотров 2159 месяцев назад
Optimizing Python Code for Better Performance - Timing objects in python (1 of 8)
Optimizing Python Code for Better Performance - Time profiling in python (2 of 8)
Просмотров 1029 месяцев назад
Optimizing Python Code for Better Performance - Time profiling in python (2 of 8)
Optimizing Python Code for Better Performance - Measuring RAM usage in python (3 of 8)
Просмотров 969 месяцев назад
Optimizing Python Code for Better Performance - Measuring RAM usage in python (3 of 8)
Great presentation, thanks! How many of the ~5,000 human enzymes have been targeted with clinical medicines? Is Lipinski's 'rule of five' still valid? He claimed there are ~500 enzymes considered "bottleneck" in biologically high impact nodules.
UniProt is probably not the first place to start looking for drug targets, and to obtain such numbers, as this is outside our field of expertise. But there are various resources that are trying to address drug targets and which are worth exploring, although they probably all define targets and druggability slightly differently: - IDG resources (Illuminating the Druggable Genome): They assign 4 different "target development levels" to drug targets: Tclin, Tchem, Tbio or Tdark. Tclin are targets for which an approved drug exists; Tchem are proteins that are not Tclin, but are known to bind small molecules with high potency, etc... (academic.oup.com/nar/article/51/D1/D1405/6851109). The PHAROS interface can be used to query the IDG data, e.g. for Tclin and Tchem pharos.nih.gov/targets?facet=Target%2BDevelopment%2BLevel!Tclin&facet=Target%2BDevelopment%2BLevel!Tchem , and to further filter this for enzymes. - DrugBank allows filtering for targets (e.g.go.drugbank.com/releases/latest#target-sequences) or enzymes. - OpenTargets www.opentargets.org/ - Human Protein Atlas (HPA) www.proteinatlas.org/humanproteome/tissue/druggable UniProtKB has cross-references to PHAROS, DrugBank, OpenTargets and HPA, and you can explore narrowing down the set of human enzymes to those entries with cross-references to one or more of these databases. Please don't hesitate to contact the UniProt helpdesk (www.uniprot.org/contact) with questions about UniProt, or directly write to the providers of the resources listed above. The UniProt team
These videos have been very helpful, is there a part 3 ?
better quality plz
how can you do a 50% and a 70% modeling?
Thanks.
Thanks.
Wonderful tool! Thanks a lot for cover up the opportunity!
super helpful, thank you
Is there any video available on how to go on refining the clustering in more detail?
Thank you for this wonderful talk! It is very insightful on the current advances of physics-informed machine learning techniques in protein-ligand interactions!
is it possible to upload this in a better quality? Thats the most importand video from the series and its hard to read in 360p
How do you get intuitively that the p of genotype error is 0.02?? I don't understand that
I am an avid user of SWISS PROT and Homology models. I have used SIB software and loved them. I would have loved to visit or see in person but I trust you guys for doing an amazing job.
Thanks.
thanks for sharing this! i see that you are analyzing group specific missing values separately from rest of data, wondering is there is an elegant way without utilizing group information?
I want to get the course material, but the link can't be opened. Could you please update the link?
I am following using the same steps but local quality estimates figure isnot porvided? what does this mean?
Thank you for sharing!
Best tutorial video. It will useful for all life science researchers. Thank you SIB.
Promo`SM ☀️
When you introduce each method, it will be great and helpful to give a comments or recommendations for each modality.
Thanks.
👍👍
i love this :)😄😄
I am new to bioinformatics, my question is what if % identity and Query coverage is less but the GMQE and Qmean score is good?, which factors are more important than the other when deciding on a good model? Again what does it mean when your swiss model has no QSQE score?
anyone can please tell me the scope of bioinformatics? how can we professionally work in this field?
Where can we access the swiss_census_1880.csv?
What are the criterias to get job in SIB
I have KYC my account but still my money is not coming out please help me
Bioinformatics is soo cool.
loved the vedio, Artistic!
Epidemics? So you are part of this scam as well? Shame on you.
Thank you very much for the excellent and informative video
Thank you! Very informative
Invest in some better audio equipment
The audio quality is poor, but it could be improved with an AI enhancement (post factum).
plz explain the repository portion in swiss model
Double descent discussed at ruclips.net/video/kCodNz3IHhU/видео.html is enlightening and scary at the same time!
hahahaaha
Kudos keep doing👍
A fun and to-the-point video. Nice job
Wow, this video makes me a proud bioinformatian ,👨🔬
Does the peptide uniqueness check consider proteolytic sites? (e.g. a match against all theoretical tryptic peptides for the human proteome?) Or is it simply matching the peptide sequences against intact protein sequences? Thanks.
Hi. I have been trying to model a fusion protein in Swiss-Model and havent suceeded. The template search only allows selection among the top 50 templates (and all happen to be the same protein) and although the complete list of templates is shown in html and .txt those lists are only descriptive ... In the "USER TEMPLATE" mode I have not succeeded either. This mode permits uploading 2 templates indeed but the model is based on just one of the templates... I need a model of the fusion protein based on the PDBs of the two proteins that are fused in my target sequence.
Dear Omar, Thank you for reaching out. We would recommend you to contact directly the group that has developed Swiss-model: www.sib.swiss/torsten-schwede-group. You can find their contact details on the webpage. Best regards, SIB Communication Team
This is literally heaven for me.
WOW, this is definitely the most coolest things kinda movie trailer about computer science!
Nice video, but it's only the first part of lecture if I understood correctly. Where is the second?
Dear Konstantin, thank you for your question and interest. This is right. The missing part, which are the practical exercises, are not in RUclips. This part is only accessible by following the course with our trainers. Here is the page where you can find the upcoming courses: www.sib.swiss/training/upcoming-training-courses Best regards, SIB Team
I wish God made me as smart as these people so I could do amazing science :(
These models are very simple and common in systems biology. It's so simple is beautiful and elegant.
man I understand what you mean. Keep it up!