NDEx News

NDEx 2.0 Q1 Update

NDEx 2.0 - Q1 Update Released!

Posted by Rudi Pillich

The first quarter of 2017 is over and the NDEx Team is ready to roll out the Q1 Update! The Q1 Update restores all of the features that had been temporarily disabled in the NDEx 2.0 release last December: bulk actions and network property editing functions are now available again while the Advanced Query function allows users to query a network...

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NDEx 2.0 Official Release!

Posted by Rudi Pillich

Less than 2 weeks have passed since the release of the NDEx 2.0 Preview Server and thanks to your support, we are proud to announce that NDEx 2.0 is READY for prime time… NDEx 2.0 is now live on our Public Server at www.ndexbio.org. Differently from previous releases, NDEx 2.0 is only available on our Public...

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NDEx 2.0 Preview is Now Live!

Posted by Rudi Pillich

We promised we were going to do it… and the NDEx Team always keeps its word! NDEx 2.0 is getting ready for prime time and we have decided to give everyone the opportunity to preview and test it before is officially released on the NDEx Public Server. The NDEx 2.0 Preview Server is a clone of...

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Integrating Knowledge from Different Sources

Posted by Rudi Pillich

The NDEx Project is involved in a collaboration with the Peter Sorger's lab as part of two DARPA-funded programs: BIG MECHANISM and COMMUNICATING WITH COMPUTERS. One output of these collaborations is The RAS Machine network, available on the NDEx Public Server and automatically updated daily. The RAS Machine integrates diverse inputs ranging from BEL curated documents, BioPAX...

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Celebrating an important milestone…

Posted by Rudi Pillich

Thanks everyone for your support…@NDExProject has 100 followers!!! Looking forward to see it growing even more… pic.twitter.com/Vn5lLnxuy1 — The NDEx Project (@NDExProject) June 1, 2016

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Improved Search

Posted by Rudi Pillich

The NDEx Team is always striving to improve and simplify our end user experience… after receiving their valuable feedback, we focused on enhancing the NDEx search feature. First of all, searching for biological networks in NDEx is now easier thanks to the addition of a "Browse" button that will let users explore the entire server's content. We also...

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Focus on Drug/Compound Networks

Posted by Rudi Pillich

In an effort to provide usable data in the form of biological networks, the NDEx Project has developed a content plan that aims to provide access to a vast array of drug/compound data from several different databases. To date, the NDEx Public Server offers a selection of networks from DrugBank, Therapeutic Target Database (TTD) and...

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NDEx v1.3 Official Release!

Posted by Rudi Pillich

"After 8 months of hard work, we have finally reached the finish line… We are proud to announce that NDEx v1.3 is officially released! We want to thank all our users and collaborators for providing valuable feedback during this long effort of development and testing." And we look forward to your continued support… Please keep...

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February newsletter

NDEx Newsletter – February 2016

Posted by Rudi Pillich

Howdy NDEx enthusiasts! In the February newsletter we announce our participation as exhibitors at ISMB 2016, feature an article about therapeutic epigenetics and remind you that the deadline for the Open Science Prize Challenge is approaching fast! >> READ OUR NEWSLETTER HERE

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The Human Interactome Unveiled…

Posted by Rudi Pillich

In living organisms, genes encode proteins and proteins form complexes, resulting in an intricate network of interactions that is responsible for orchestrating all biological cellular processes. The human genome has around 20,000 protein-coding genes and only a small fraction of these proteins has been characterized at the functional level… For this reason, a new project led...

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NDEx Newsletter – January 2016

Posted by Rudi Pillich

Happy New Year from the NDEx Team! In the first newsletter of 2016 we describe a new knowledge base for naturally occurring venoms, feature an article about bioinformatic resource funding and remind you to come check us out at the XXVI Plant and Animal Genome (PAG) conference in sunny (not so much lately) San Diego!...

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NDEx Newsletter – December 2015

Posted by Rudi Pillich

The December newsletter is all about the NDEx v1.3 Release candidate! Several new features and architectural changes characterize the new NDEx v1.3… Learn more about the CX interchange format and the future of the Cytoscape Cyberinfrastructure. >> READ OUR NEWSLETTER HERE

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The Melanoma Gene Database

Posted by Rudi Pillich

Melanoma is one of the most aggressive human cancers. Similar to many other cancers, melanoma is initiated by activation of oncogenes or inactivation of tumor suppressor genes. However, there is no database available yet focusing on genes involved in melanoma causation. In this view, Dr. Zhang and collaborators have manually curated a vast body of literature and created...

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Cover of Cell systems, issue 4, October 28, 2015

NDEx Newsletter – November 2015

Posted by Rudi Pillich

This month we focus on the NDEx Publication now available on Cell Systems, we announce a new collaboration that will bring plant networks to NDEx and feature the International Mouse Phenotyping Consortium (IMPC). >> READ OUR NEWSLETTER HERE We want to hear your voice… Give us your feedback and help us improve NDEx! Connect with us...

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The NDEx paper available online on the Cell Systems journal website

The NDEx publication is out!

Posted by Rudi Pillich

The NDEx Team is proud to announce that the first NDEx paper has been published in the October 28 issue of "Cell Systems". Two full years of work, meetings, testing and constant interaction with users and stakeholders have helped us reach this important milestone… Thanks everyone for your hard work! And we are sure you...

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Looking for biologist-oriented analytic tools? Introducing METASCAPE!

Posted by Rudi Pillich

Technology advancements provide access to huge amounts of data and today's scientists biggest obstacle is to analyze these data sets in order to make meaningful data-driven decisions. Most importantly, the analytic tools need to be simple enough to be used by biologists that often lack advanced bioinformatic skills; tasks such as annotating a gene list or performing ID conversion...

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NDEx Newsletter – October 2015

Posted by Rudi Pillich

The NDEx Project is happy to announce that the October Newsletter is out! In this month's news from the NDEx Team we offer you the opportunity to transform your datasets into novel networks, we feature a nifty tool for literature and web research and link to an interesting article on mining cell line names in scientific...

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Molecular double-cross?

Posted by Rudi Pillich

Rb, p53, PTEN… Many genes are known for their ability to keep cancer under control thus acting as tumor suppressors. But what if a tumor suppressor gene could also act as an oncogene and stimulate cancer growth rather than inhibiting it? Are we looking at a new class of "double-cross" genetic elements? A new article...

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The NDEx Newsletter – September 2015

Posted by Rudi Pillich

The NDEx Project is glad to announce that the September newsletter is out!!! This month we show some amazing performance improvements that you can expect in our next release, NDEx v1.3, later in Q1 2016. We also feature an interesting research article by Bikel and collaborators focused on the human microbiome. Finally, we present an...

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Interactive Networks viewer – Phase 1 complete!

Posted by Rudi Pillich

Elsevier and Cytoscape have joined forces to create a networks viewer that allows authors to publish fully interactive network diagrams as part of their articles on ScienceDirect.com. Detailed instructions for authors and links to publications that use this new feature are available here. As of phase 1, the interactive viewer allows some basic actions like moving nodes and...

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NDEx v1.2 Official Release!

Posted by Rudi Pillich

The NDEx Team is proud to announce that NDEx v1.2 is now available on our Test and Public servers as well as on our FTP site for all who prefer to install and run their own, private NDEx server instance. The NDEx v1.2 release has many new features, changes in the user interface and improvements to boost stability as well as functionality; therefore, we strongly recommend a careful review of our documentation for...

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NDEx Newsletter – June 2015

Posted by Rudi Pillich

Howdy!!! The NDEx Team would like to share some news and hopes you'll find it interesting! Follow us on LinkedIn or visit our website to stay informed on new project features, releases and other interesting content and subscribe to our YouTube channel! Questions? Comments? We ‘d be happy to hear from you! NDEx v1.2 Release Candidate...

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TRIBE: collaboration and data mining

Posted by Rudi Pillich

Tribe is a collaborative platform that allows mining of big data across bioinformatics systems. Here at the NDEx Project, we are excited to find a system with a similar philosophy and complementary content. Tribe has features that make it an interesting resource for both biology and bioinformatics researchers and we look forward to evaluating it...

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NDEx Newsletter – May 2015

Posted by Rudi Pillich

Howdy !!! The NDEx Team would like to share some news and hopes you'll find it interesting! Follow us on LinkedIn, subscribe to our Youtube channel and visit our website to stay informed on new project features, releases and other interesting content! Questions? Comments? We ‘d be happy to hear from you! The new "NDEx...

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1st "BD2K" / 3rd "Network of BioThings" hackathon at The Scripps Research Institute

Posted by Rudi Pillich

Hello Past & Future Hackers!!! TSRI is hosting a BD2K / "Network of BioThings" hackathon May 7-9th 2015. The purpose of this hackathon is to bring together experts in their respective fields to collectively work on solving challenges related to biomedical big data. This hackathon will feature networking and mentoring with leading researchers and experts,...

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Welcome to Vladimir Rynkov!

Posted by Rudi Pillich

The NDEx Team keeps growing… Vladimir Rynkov, our new software engineer, will join efforts with Jing Chen to develop/manage the NDEx back-end, ensure that our servers run smooth and guarantee a solid performance. Check out out team members page for more information about Vladimir's background and experience!

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Spring forward!

Posted by Rudi Pillich

It's that time of the year… and the NDEx Project is ready to spring forward to provide new features and content to the scientific community! On March 6th, 2015 we updated the NDEx Public Server to the latest version (1.2 Alpha), bringing to you enhanced stability and performance, several UI changes for an improved user experience...

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Save the date… A taste of NDEx v1.2!

Posted by Rudi Pillich

The NDEx Team is right on schedule for the release of NDEx v1.2 in Q2 2015 and has decided to make an NDEx v1.2 alpha version available for you to evaluate! Explore and start enjoying some of the great improvements you will see in the final NDEx v1.2. Besides improved server stability, scalability and performance,...

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Looking for articles or conferences?

Posted by Rudi Pillich

In an effort to provide even more resources to our scientific community, the NDEx Project now provides links to publications focused on network biology as well as relevant conferences coming up in 2015! The list of Network Biology publications is maintained on Tumblr by the Network Biology Group. These useful resources can be conveniently accessed from the home page of...

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Content content content!!!

Posted by Rudi Pillich

The NDEx Project aims to become a main hub for storing, sharing and publishing biological network data and a very important part of our efforts is focused on providing interesting, valuable and re-usable content to enable interaction and collaboration within the scientific community worldwide. We recently updated the NDEx database to include the latest "Extended...

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Welcome to Dr. Chen!

Posted by Rudi Pillich

The NDEx Project is happy to announce that his Lead Software Engineer, Dr. Jing Chen, has officially joined the NDEx Development Team on a full time basis! Dr. Chen has many years of experience in software development focused on the integration and management of life science data. Prior to joining the NDEx Team, Dr. Chen worked at...

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NDEx v1.1 Official Release announced

Posted by Rudi Pillich

The NDEx Team has announced that NDEx v1.1 will be officially released in January 2015. New features include but are not limited to: Lucene indexing for network searches and queries, an improved web UI and a brand new, user oriented Informational Website with tutorials, technical resources, news and more! The release of NDEx v1.1 will...

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Cytoscape v3.2 is here!

Posted by Rudi Pillich

The Cytoscape team worked hard to bring v3.2 right at your fingertips !!! Faster startup, experimental support for Java 8, interactive web visualization, chart editor, gradient effects and a lot more… Download Cytoscape 3.2 and discover all the new features available!

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