Bina Bloggers

Free NGS Webinar: An Ensemble Approach with Machine Learning to Detect Cancer Variants

Posted by Jenny Hsu on May 12, 2016 10:00:00 AM

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Time & Date:

REGISTER TO JOIN US on Thursday June 16, 2016, 10 am PT // 1 pm ET.

SOMATICSEQ: AN ENSEMBLE APPROACH WITH MACHINE LEARNING TO DETECT SOMATIC MUTATION DETECTION

Accurate detection of somatic mutations has proven to be challenging in cancer NGS analysis, due to tumor heterogeneity and cross-contamination between tumor and matched normal samples. Oftentimes, a somatic caller that performs well for one tumor may not for another.

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Topics: Somatic Mutation Detection, Bina Tools & Workflows, Webinar, Bina GMS, BioIT, SomaticSeq, NGS, VarScan, SomaticIndelDetector, VarDict, MuTect, SomaticSniper

VarDict: A Somatic Variant Caller Available in the Bina RAVE Software

Posted by Anoop Grewal on May 10, 2016 10:00:00 AM

somaticfinal.pngDetails on Vardict, a new variant caller, have been published recently in Nucleic Acids Research by authors, Zhongwu Lai and Jonathan Dry, among others from AstraZeneca [1]. The current version of the Bina Read Alignment Variant Calling and Expression software module for secondary analysis includes Vardict, along with five other tools, for calling SNVs or indels from tumor-normal pairs. As the article demonstrates, VarDict has multiple strengths that extend our capabilities in variant calling beyond what was available before its release. Notably, the algorithm is particularly good at detecting indels. It also handles ultra-deep sequenced samples, which have become more common of late, and supports variant calling in tumor-only samples (in addition to tumor-vs-normal calling).

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Topics: DREAM Challenge Results, Somatic Mutation Detection, Tumor-Normal, Webinar, Bina RAVE, SomaticSeq, AstraZeneca, Sequencing, VarScan, JointSNVMix, SomaticIndelDetector, VarDict, MuTect, SomaticSniper

Welcome to Bina's New Library

Posted by Farzan Naimi on May 5, 2016 10:00:00 AM

At the beginning of the year, we launched the Bina Science section on our website to showcase open source algorithms and peer reviewed journal articles that our team has produced. We are excited to announce the latest addition to our website, the Bina Library. We invite you to explore white papers and poster presentations, watch webinars and case study videos, and learn more about how our products can help you advance genomic discoveries. Simply choose the media type or topic at the top of the page to get started with discovering what we have in our library.

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Topics: Whitepaper, Webinar, Videos, website, Poster, Presentation, Library

Webcast On Demand - Genomics Data: Challenges and Opportunities

Posted by Jenny Hsu on Dec 15, 2015 10:30:00 AM

For those who missed our panel discussion in the "Enabling Genomics Data" track at the Festival of Genomics San Mateo last month, you can now catch the webcast replay on demand

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Topics: Events & Conferences, Webinar, Festival of Genomics

SomaticSeq Webinar Now Available on Demand

Posted by Jenny Hsu on Dec 10, 2015 10:30:00 AM


Did you miss last week’s webinar on SomaticSeq? It’s now available on demand. Watch it to learn how we used this newly published ensemble and machine learning approach to score first in indel calling and second in SNV calling in the recent ICGC-TCGA DREAM Somatic Mutation Calling Challenge.

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Topics: DREAM Challenge Results, Somatic Mutation Detection, Bina Tools & Workflows, Cancer, Webinar, RAVE, SomaticSeq

Webcast: Genomics Data - Challenges and Opportunities

Posted by Jenny Hsu on Nov 24, 2015 12:29:18 PM


Did you miss out on the Festival of Genomics California this month, or was at the conference but didn’t make it to the “Enabling Genomic Data” session? We are excited to bring a broadcast of our panel discussion on “Genomics data - Challenges and opportunities” to you next Tuesday, December 1st at 9am PT // 12 noon ET // 5pm GMT.

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Topics: Webinar, Festival of Genomics, Data Challenges

Free Webinar: An ensemble and machine learning approach to accurately detect somatic mutations

Posted by Jenny Hsu on Nov 17, 2015 9:30:00 AM

Leading the latest DREAM challenge using an ensemble and machine learning approach to somatic mutation detection

Accurate detection of somatic mutations has proven to be challenging in cancer NGS analysis, due to tumor heterogeneity and cross-contamination between tumor and matched normal samples. Oftentimes, a somatic caller that performs well for one tumor may not for another.

Read More

Topics: DREAM Challenge Results, Somatic Mutation Detection, Webinar

Free Webinar: A unified approach for optimizing RNA-Seq alignment and junction detection

Posted by Jenny Hsu on Sep 10, 2015 9:00:00 AM

The development of high-throughput methods for transcriptome sequencing (RNA-Seq) has offered a means to measure gene expression across broader dynamic ranges and to identify novel alternate transcripts. Out of a plethora of tools available, a few have been carefully chosen to be integrated into Bina RAVE, a robust solution for secondary NGS analysis.

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Topics: Webinar, RAVE, RNA-Seq

Free Webinar: MetaSV - An Accurate and Integrative Structural-Variant Caller for NGS Data

Posted by Jenny Hsu on Aug 18, 2015 9:00:00 AM

Structural variations (SVs) are said to contribute to genomic diversity as well as genomic disorders. Due to their varying lengths, accurate detection of SVs has been challenging with the relatively short-reads generated from next-gen sequencing.

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Topics: Webinar, RAVE, structural variation

Free Webinar: Mining Somatic Variants in Cancer Exomes Utilizing Bina AAiM Software Module

Posted by Jenny Hsu on Jul 9, 2015 9:00:00 AM

The use of next generation sequencing (NGS) data has grown rapidly in many areas of scientific and clinical research. Extracting biological meaning from the large numbers of variants identified in these studies, however, remains a significant challenge.

The Bina Annotation and Analytics Intelligence Module (Bina AAiM) is an efficient, scalable, and easy-to-use system for investigating and prioritizing variants from NGS analyses, along with extensive visualization capabilities to aid in interpretation.

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Topics: Cancer, Webinar, AAiM, Annotation

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