The NDEx Project

Developed @UCSanDiego, NDEx is an open source software infrastructure to store, share and publish biological network knowledge

[The NDEx Project @NDExProject]

We did it!
Cytoscape Web v1.0 is live!
Try it here: https://t.co/saGA9z98A3

Publication: https://t.co/iPPbqfbAJF
Manual: https://t.co/mRvBe33xR8

#BiomedicalResearch #SystemsBiology

[The NDEx Project @NDExProject]

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. https://t.co/PSnvoO9QwE

[The NDEx Project @NDExProject]

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

[Elizabeth McKenna @ElizSMcKenna]

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 https://t.co/gAw1xSwDri @UCSanDiego @UCSDCancer #MachineLearning

[EMBL-EBI @emblebi]

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👇

https://t.co/hzeoYAFdwH

[nature @Nature]

In a world first, the UK medicines regulator has approved a therapy that uses CRISPR gene editing as a treatment for diseases https://t.co/Lk7eZ4Tkiz

[Bioconductor @Bioconductor]

**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: https://t.co/X5UFDaHw7I

[The NDEx Project @NDExProject]

@ASMicrobiology Salmonella?

[UniProt @uniprot]

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 https://t.co/HhCpyy4oOX
16 Nov 2023, 15:30-16:30 (UK) @EBItraining

[The NDEx Project @NDExProject]

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

[Dr. Tijana Milenkovic @ProfMilenkovic]

Our review+perspective paper on "Current and future directions in network biology" is online (https://t.co/CbgF5Wir5Z). This has been a Herculean effort by many co-authors, thank you all! Special thanks to @marinkazitnik, @_michellemli, @aydin_wells, and all section coordinators.

[The NDEx Project @NDExProject]

Our preprint is out!
Learn how #LLMs can help you discover gene set function: https://t.co/22aGLy7wuL

#nciitcr #networkbiology @cytoscape @CancerCellMap @NCIsysbio @UCSanDiego @BCMFromtheLabs

[Conzept @conzept__]

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: https://t.co/DngvofcJwt

Explore all the human protein encoding genes: https://t.co/aKKGSLTzir

[The NDEx Project @NDExProject]

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 !

https://t.co/gXM4RmzAKN

@cytoscape @ucsdccbb @CancerCellMap #NCIITCR

[Eduard Porta @eportacangen]

Super excited to share with you the results of the CPTAC PanCancer Driver project, today officially out at @cellcellpress!

https://t.co/qGN3KBeu4d

Here’s a short tweetorial with the main findings where our lab mostly contributed

[Steven Ge @StevenXGe]

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 https://t.co/pjY000GMBu

[CoSy.Bio @cosybio_UHH]

#DrugstOne: Turn your #Bioinformatics tool into a powerful, interactive #DrugRrepurposing 💊 webtool in <15mins with 3 lines of code. Check out https://t.co/lPZHkKdF9E and join our initiative and publication (https://t.co/0RE5JVn6Nt). @janbaumbach @MichiHartung @MajoreAndi

[dkNET @dkNET_Info]

The deadline was extended - so students, don’t wait!
The dkNET Summer of Data Student Program applications are due May 8, 2023! (https://t.co/LfnMBqq5Lk)
#FAIRdata #OpenScience #reproducibility #rigor

[Signaling Pathways Project @sigpathproject]

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 https://t.co/VHF45SjA44

[Chris Mungall @chrismungall]

We have released version 0.3.0 of the #OntologyAccessKit #oaklib https://t.co/srPUPfN0dH. Includes preliminary compatibility with cytoscape CX format and @NDExProject, upgrade to the latest @bioregistry, and more support for working with the @OBOFoundry #RelationOntology!