Developed @UCSanDiego, NDEx is an open source software infrastructure to store, share and publish biological network knowledge
La Jolla, CA
Joined September 2015
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We did it!
Cytoscape Web v1.0 is live!
Try it here: web.cytoscape.org
Publication: doi.org/10.1093/nar/gkaf365
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
The NDEx Project retweeted
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/10.1158/2159-8290.CD… @UCSanDiego @UCSDCancer #MachineLearning
The NDEx Project retweeted
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/bioinformat…
ALT Title and authors of a journal article
The NDEx Project retweeted
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
The NDEx Project retweeted
**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
ALT Moving Platforms Post for Bioconductor
The NDEx Project retweeted
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/events/pr…
16 Nov 2023, 15:30-16:30 (UK) @EBItraining
The NDEx Project retweeted
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.2309.…
#nciitcr #networkbiology @cytoscape @CancerCellMap @NCIsysbio @UCSanDiego @BCMFromtheLabs
The NDEx Project retweeted
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/Calumenin?l…
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
The NDEx Project retweeted
Super excited to share with you the results of the CPTAC PanCancer Driver project, today officially out at @cellcellpress!
sciencedirect.com/science/ar…
Here’s a short tweetorial with the main findings where our lab mostly contributed
The NDEx Project retweeted
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/ploscompbi…
The NDEx Project retweeted
#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 NDEx Project retweeted
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-Progr…)
#FAIRdata #OpenScience #reproducibility #rigor
The NDEx Project retweeted
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
The NDEx Project retweeted
We have released version 0.3.0 of the #OntologyAccessKit #oaklib github.com/INCATools/ontolog…. Includes preliminary compatibility with cytoscape CX format and @NDExProject, upgrade to the latest @bioregistry, and more support for working with the @OBOFoundry #RelationOntology!
The NDEx Project retweeted
Can't recommend this free 2-day #GeneOntology workshop enough!! If you can get to Rome the week after #biocuration2023, sign up now. Space is limited and yes the instructors are absolutely fantastic! @UCLgene @MINT_database
Join the Rome-UCL bioinformatics workshop in May @BiologiaUniRM2 with Ruth Lovering @UCLgene and Luana Licata @MINT_database
Registration free but essential: tinyurl.com/UCL-Rome-bioinfo…
The NDEx Project retweeted
I'm hiring for a position in the software development team at the Ideker Lab, UC San Diego. The position is closely integrated with the research in the lab and also the @cytoscape and @NDExProject projects. employment.ucsd.edu/research…