Author Archives: NextBio

Query curiosity: NextBio queries using biosets

Posted on January 30, 2012 by NextBio. Filed under Tutorials

In Part III of the NextBio tutorials, we demo bioset queries with the Curated Studies, Biogroups and Genome Browser apps

Incorporating different kinds of data into a single system means that every experiment included has to be normalized and compared with other curated studies in the NextBio platform. One way we accomplish this is by standardizing different kinds of results into biosets.

A bioset usually represents the results from a single experiment. For this tutorial video, we used a bioset that compares colon cancer cells that have metastasized to the liver to normal liver tissue.  The tutorial walks you through using this bioset to query Biogroups, which shows groups of genes or pathways that are enriched in this particular comparison.   Read more…

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NextBio Public Tutorials: Exploring the experimental details behind NextBio results

Posted on November 30, 2011 by NextBio. Filed under Tutorials

In part II of the NextBio Public tutorials, we show you how to find the experimental details underlying your NextBio query results.

Critics of GWAS are quick to point out that the genetic associations identified in such studies rarely reach clinical significance. However, integrating associations identified in genome-wide studies with evidence from more directed experiments can speed up the process of taking genomic variants from the bench to the clinic. Watch our tutorial to find out how to dig down into the experimental results associated with a gene query in NextBio, or read on to learn more about our study* on one particular gene, POU5F1B. Read more…

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NextBio Public Video Tutorials: Using NextBio to explore a gene

Posted on October 31, 2011 by NextBio. Filed under Tutorials

In part I of the NextBio tutorials, we explain how and why NextBio helps explore data relevant to a gene query

A single gene can be studied in many ways-   genome-wide analysis for associations with diseases, experimental studies of function in cell lines or animal models, or pharmaceutical research as a potential drug target. At NextBio, we aggregate these diverse kinds of data, normalize and integrate them on a common platform, coalescing diffuse “data clouds” to address focused research questions.

In the first of our NextBio Public tutorials, we explain how to use simple NextBio functions to find this aggregated data relevant to a gene, beginning with GWAS associations, to descriptions of tissues and cell lines and results from pharmacological experiments, all in a matter of minutes.

Read more…

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Crowdsourcing solutions for life

Posted on October 21, 2011 by NextBio. Filed under Conferences, Guest Blogger, Open Science

From the lab to scientific publishing to clinical solutions, the Open Access movement is changing the way science advances

(Guest post by Joseph Jackson)

The 2nd Open Science Summit is the weekend of October 22-23, 2011 at the Computer History Museum in Mountain View, just before the 2011 Open Access (OA) week, which runs October 24th-28th.  Open Science evokes different associations for different people, depending on which part of the scientific process they most regularly engage with.  One critical component focuses on access to scientific literature.  The OA movement has made great strides in the last ten years with the creation and maturation of journals and publishers like PLoS and Biomed Central.

But the most critical shifts toward Open Science arguably are happening in the life sciences.  The technological revolution underway in next generation sequencing is enabling, but also requiring bold new collaborative approaches to manage increasing complexity and accelerate the translation of scientific discoveries into desperately needed therapies.
Read more…

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Quiz winner!

Posted on August 24, 2011 by NextBio. Filed under Contests

If you haven’t already, check out our first blog quiz. Though the contest is closed, you’re still welcome to guess the answers! For the curious, the correct answers are included here.

Though we’d announced multiple prizes, only one entrant got all the right answers: Congratulations (once again) Dave Schlesinger!

The answers:

1. The Translational Genomics Research Institute

2. MCU

3. Paroxetine

4. Sepandar Kamvar

5. No one knows

6. All of them

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Blog quizzes are here!

Posted on August 15, 2011 by NextBio. Filed under Contests, NextBio

Back for more excitement? We hope you’ve been following us closely, because this blog now has contests (with Rules, even), prizes and now, a quiz!

All these answers are on the blog. Think you can find them? Take our quiz and find out! All participants’ names will be entered in a drawing for one of three gift cards from Starbucks, Amazon or iTunes (your choice!). Entries must be received by August 19, 2011 to be eligible for prizes.

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Ready, set, go!

Posted on July 29, 2011 by NextBio. Filed under News

Remember when we said we had big news to share? It’s almost here! As we get closer to launching our public site, share in our excitement by entering the contests and prize drawings we’ll be announcing in this space over the next few weeks.

Join us every single week for another chance to win, or just drop by and participate when you like- there’s no obligation necessary (Either way, don’t miss the Official Rules first). And once our public site is up, come back for our biggest contest of the year: the NextBio Genomics Innovation Challenge.

At NextBio, we like to look at data with fresh eyes. We know that integrating diverse kinds of information with strong data mining strategies can yield fresh hypotheses, new insights and much more. With the data accessible and the most intuitive, user-friendly tools possible, brand new genomic discoveries are just waiting to be made. The NextBio Genomic Innovation Challenge is your chance to do it. And if intellectual satisfaction isn’t thrilling enough for you, there are big prizes to be won as well. Watch this space to find out more. And as you wait for the public site and bigger prizes, why not try your hand at a few other contests too?

For starters, we’ll keep it really simple- all you have to do is keep in touch! First, like us on Facebook and second, drop us a line. Leave us a comment either on this blog post or on our Facebook Wall, telling us about your research interests. Do both (Follow us on Facebook AND leave a comment) by August 5, 2011 August 10, 2011 and your name will be entered in a drawing for one of three gift cards ($10.00 each) from Starbucks, Amazon or iTunes (your choice!).

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The newest addition to NextBio Publications

Posted on October 5, 2010 by NextBio. Filed under NextBio

If you’ve looked at our NextBio Publications page lately, you’ve probably noticed that the list of publications from authors who have used NextBio to make novel connections is growing at a steady pace. To this, we add a publication from the Scientific and Computational Biology group at NextBio itself:

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data
Ilya Kupershmidt, Qiaojuan Jane Su, Anoop Grewal, Suman Sundaresh, Inbal Halperin, James Flynn, Mamatha Shekar, Helen Wang, Jenny Park, Wenwu Cui, Gregory D. Wall, Robert Wisotzkey, Satnam Alag, Saeid Akhtari, Mostafa Ronaghi
PLoS ONE 5(9): e13066. doi:10.1371/journal.pone.0013066

In this article, we explain our processes for data curation and the computational methods by which signatures are compared in NextBio to yield novel findings. We also include four use cases that illustrate how this all comes together for the purpose of investigating brown preadipocytes and brown fat lineage. We hope you find the paper illustrative of how you can apply NextBio’s platform to discovery in your area of research. And don’t forget to include this publication in your citation when you make novel discoveries using NextBio.

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