The NDEx Project

We did it! Cytoscape Web v1.0 is live! Try it here: web.cytoscape.org Publication: doi.org/10.1093/nar/gk… Manual: web-manual.cytoscape.org #BiomedicalResearch #SystemsBiology

We’re excited to be officially included in the #NIAID Data Ecosystem Discovery Portal, a hub for accessing #FAIRData from over 50 sources related to infectious and immune-mediated diseases. data.niaid.nih.gov

NDEx v2.5.8 is out. Still working with the @news4go team to include their GO-CAMs in IQuery... And the @cytoscape Web beta is coming soon! Stay tuned for the official announcement. #networkbiology #nciitcr @CancerCellMap @CancerSysBio @ucsdccbb

Now online in @CD_AACR: Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress - by @Xiaoyu_SysBio @aksinghal90 @TreyIdeker and colleagues doi.org/10.1158/2159-8… @UCSanDiego @UCSDCancer #MachineLearning

Looking for a new way to measure impact metrics for your database? Introducing MBDBMetrics; an online tool designed to measure the impact of any biological data resource, freely accessible via Google Colab and GitHub. Find out more and try MBDBMetrics👇 academic.oup.com/bioinformatics…

In a world first, the UK medicines regulator has approved a therapy that uses CRISPR gene editing as a treatment for diseases go.nature.com/3QDtwuV

**We are moving platforms** Bioconductor will cease posting on Twitter/X as of December 17, 2023. Instead we will be continuing to post on other social media platforms that better reflect our community’s code of conduct. Read more in our blog post: buff.ly/3RddEAV

@ASMicrobiology Salmonella?

#MicrobeoftheMonth! Who am I? 1) I'm commonly associated with shellfish. 2) I can cause gastrointestinal and wound infections. 3) Due to climate change, the number of infections I cause is expected to rise. Think you know? Comment below!

Interested in programmatic access to the UniProt database using Python - protein entry searches, data filtering, batch downloads & further processing of downloaded target data? Sign up for our next free webinar ebi.ac.uk/training/event… 16 Nov 2023, 15:30-16:30 (UK) @EBItraining

@PhysInHistory Science is the "human" attempt to explain and fit-in-a box what took billions of years to create and evolve.

Science doesn't purvey absolute truth. Science is a mechanism. It's a way of trying to improve your knowledge of nature. It's a system for testing your thoughts against the universe and seeing whether they match. And this works, not just for the ordinary aspects of science, but for all of life. I should think people would want to know that what they know is truly what the universe is like, or at least as close as they can get to it. -- Isaac Asimov, as mentioned in a 1988 interview by Bill Moyers

Our review+perspective paper on "Current and future directions in network biology" is online (arxiv.org/abs/2309.08478). This has been a Herculean effort by many co-authors, thank you all! Special thanks to @marinkazitnik, @_michellemli, @aydin_wells, and all section coordinators.

Our preprint is out! Learn how #LLMs can help you discover gene set function: doi.org/10.48550/arXiv… #nciitcr #networkbiology @cytoscape @CancerCellMap @NCIsysbio @UCSanDiego @BCMFromtheLabs

Improved the @NDExProject linking. Now linked via the @HGNC gene symbol, instead of the name. The range of #protein path visualizations presented is truly impressive. Link: conze.pt/explore/Calume… Explore all the human protein encoding genes: tinyurl.com/52fzfwx3

Curious about the current status of @NDExProject ? Wondering how to use our infrastructure or collaborate with us? Find out in our latest video presentation crafted for #ismbeccb2023 ! youtu.be/uyb1kITH0Ns @cytoscape @ucsdccbb @CancerCellMap #NCIITCR

Super excited to share with you the results of the CPTAC PanCancer Driver project, today officially out at @cellcellpress! sciencedirect.com/science/articl… Here’s a short tweetorial with the main findings where our lab mostly contributed

Top 50 most popular tools for pathway analysis. 1. Overrepresentation analysis (ORA) using a gene list 2. Functional class scoring (FCS) using expression data or some metrics. Based on a survey by @mdziemann's group journals.plos.org/ploscompbiol/a…

#DrugstOne: Turn your #Bioinformatics tool into a powerful, interactive #DrugRrepurposing 💊 webtool in <15mins with 3 lines of code. Check out drugst.one/call/ and join our initiative and publication (arxiv.org/abs/2305.15453). @janbaumbach @MichiHartung @MajoreAndi

The deadline was extended - so students, don’t wait! The dkNET Summer of Data Student Program applications are due May 8, 2023! (dknet.org/about/Summer-P…) #FAIRdata #OpenScience #reproducibility #rigor

Ever seen ads for #taltz on TV and wondered what its MOA is in resolving psoriasis? Wonder no more - collaborating with @EliLilly and @NDExProject we show how Taltz blocks an IL17A-MuvB pathway to inhibit keratinocyte proliferation in clinical #psoriasis bit.ly/3JVUKcU

We have released version 0.3.0 of the #OntologyAccessKit #oaklib github.com/INCATools/onto…. Includes preliminary compatibility with cytoscape CX format and @NDExProject, upgrade to the latest @bioregistry, and more support for working with the @OBOFoundry #RelationOntology!