Apr
1
Apr 5

AACR Annual Meeting 2017

  • Walter E. Washington Convention Center

 

Meeting Homepage

The CGC Team will be at the American Association for Cancer Research Annual Meeting 2017 in Washington, D.C.

 


Mar
19
Mar 23

Keystone Symposia: Cancer Immunology and Immunotherapy 2017

  • Fairmont Chateau Whistler, Whistler, British Columbia, Canada

Meeting Homepage

The CGC Team will be at the Keystone Symposia 2017 in Whistler, British Columbia, Canada. 

At the Poster Session 1 on Monday, March 20th, Dr. Jack DiGiovanna will be presenting, "Activating the immune system: population responses to immunotherapy and novel workflows for neoantigen prioritization." 

 

Feb
19
Feb 24

Tri-CON 2017

  • Moscone North Convention Center

Meeting Homepage

The CGC Team will be at Molecular Med Tri-CON 2017 in San Francisco, CA.  

On Monday, February 20th, at 4:10pm, Dr. Gaurav Kaushik will be giving a talk titled "The Cancer Genomics Cloud (CGC), part of the NCI Cloud Pilot project, democratizes access to The Cancer Genome Atlas, one of the world’s largest cancer genomics datasets. The CGC removes the need to download data, enables easy querying, and provides computational resources for custom analyses. We discuss its design and the avenues of discovery which it enables."

 

 

Jan
17
Jan 19

Cancer Genomics Cloud Seminar and Workshop 2017

  • Universidad de Chile in Santiago, Chile

The CGC Team will be at the Universidad de Chile in Santiago, Chile. 

Dr. Erik Lehnert and Dr. Jacqueline Rosains will be giving a Cancer Genomics Cloud seminar and leading a two-day workshop for biologists, bioinformaticians, and clinicians.

 

Jan
3
Jan 7

Pacific Symposium on Biocomputing 2017

  • Fairmont Orchid, Kohala Coast, Big Island, Hawaii

Meeting Homepage

The CGC Team will be attending the PSB 2017 in Big Island, Hawaii. 

Dr. Gaurav Kaushik will be presenting "Rabix: An Open - Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions" at the Methods to Ensure the Reproducibility of Biomedical Research session on Friday, January 6th at 9:35am.

Dec
7
9:00 am09:00

Cancer Genomics Cloud Seminar 2016

  • Genomics Institute Singapore

The CGC Team will be at the Genomics Institute Singapore. 

Dr. Gaurav Kaushik will present on the NCI Cancer Cloud Pilot program and the Seven Bridges Cancer Genomics Cloud to cancer researchers and trainees.

Nov
1
Nov 4

Common Workflow Language Meetup 2016

  • London UK

The CGC Team will be attending a meetup with the Common Workflow Language Community, which will include outreach and collecting feedback from the developer community.

Oct
24
9:00 am09:00

Cancer Genomics Cloud Workshop 2016

  • UC San Diego

The CGC Team is giving UC San Diego students from the MD/PhD program a three hour seminar and workshop on the Cancer Genomics Cloud.  Topics include RNA Sequencing, methylation array data analysis, processing, visualization, and predictive modeling.

Sep
21
Sep 22

Wolfram Data Summit 2016

  • Hyatt Regency Fairfax

The CGC Team will be at the Wolfram Data Summit in Fairfax, Virginia. Dr. Jack DiGiovanna will be giving a talk entitled "Leveling the playing field for cancer genomics," which describes how a unified data model was created across diseases in the TCGA dataset and the research applications that this metadata ontology and semantic triple-stores enable, including straightforward tumor-normal and pan-cancer analysis.

Sep
19
Sep 22

Festival of Genomics California

  • San Diego Convention Center

The Cancer Genomics Cloud team will be at the 2016 Festival of Genomics California.

Dr. Jack DiGiovanna will be giving a talk titled "Precision Medicine in the Million Genome Era" and Dr. Gaurav Kaushik will be speaking on "Harmonizing All Data Underlying Precision Medicine". Each talk will touch upon our experiences in building and iterating on the Cancer Genomics Cloud and how to enable research and medicine through democratized data and computing resources. 

Sep
13
1:00 pm13:00

DREAM Challenge Webinar #2

  • https://global.gotomeeting.com/join/893106749

The CGC Team is hosting a two-part webinar series that will focus on getting started with the DREAM Challenge. Researchers wanting to participate in the DREAM Challenge or who wish to learn more about accurate, reproducible RNA Sequencing analysis are encouraged to attend.

The second webinar, on Tuesday September 13th at 1pm EDT, will focus on:

  • Using the API to programmatically access resources and test algorithms
  • Automate the evaluation of tools on all training data in Python

LINK TO WEBINAR STREAM (will go live at 12:50pm EDT on 9/13): https://global.gotomeeting.com/join/893106749

You can also dial in using your phone:
United States : +1 (408) 650-3123
Access Code: 893-106-749

 

Sep
9
1:00 pm13:00

DREAM Challenge Webinar #1

  • https://global.gotomeeting.com/join/264744749

The CGC Team is hosting a two-part webinar series that will focus on getting started with the DREAM Challenge. Researchers wanting to participate in the DREAM Challenge or who wish to learn more about accurate, reproducible RNA Sequencing analysis are encouraged to attend.

The first webinar, on Friday September 9th at 1pm EDT, will cover:

  • Deploying tools and workflows with the CGC SDK 
  • Evaluating their performance with DREAM Challenge data through the visual interface

LINK TO WEBINAR STREAM (will go live at 12:50pm EDT on 9/9): https://global.gotomeeting.com/join/264744749

You can also dial in using your phone: 
United States +1 (408) 650-3123
Access Code: 264-744-749 

Aug
19
1:00 pm13:00

Bring your own data workshop

The Cancer Genomics Cloud team is hosting a  “Bring Your Own Data” workshop, focused on RNA Sequencing analysis on Aug. 19th from 1 to 5pm at the Seven Bridges office in Cambridge, MA. We hope that you can attend!

For this workshop we will be trying something different - call it a clinic: you’ll bring and analyze your own data.  We will demonstrate how to build and run a custom RNA-Seq analysis workflow in which we align your reads against a reference, obtain gene-level counts, and perform differential expression all on the CGC. At the conclusion, you’ll be able to extend your analysis to any other data, including TCGA.

If you’re able to attend, please fill out this Google form by August 12th to reserve your place and receive instructions on how to upload your data in advance of the workshop.

Learn More

Jul
9
8:30 am08:30

ISMB 2016 Applied Knowledge Exchange Session (AKES)

  • Swan and Dolphin Hotel

Meeting Homepage

Reproducibility remains a major concern in biomedical research. Recently, it has been demonstrated that cancer informatics analyses performed within a single consortia may yield wildly variable results. As the collection of genomic data and analyses continue to accelerate, concerns about maintaining the accuracy of results continues to grow. Large-scale, accurate cancer analyses demand scalable informatics. Scalability in turn requires reproducibility and portability of tools, analyses, and data to ensure that researchers can collaborate easily and effectively.

Recent technological developments and organizational efforts have sought to address the reproducibility problem in biomedical data analysis and have been successfully applied to cancer informatics. For example, Docker containers enable researchers to package software with all of its required dependencies and nothing more. This feature allows software to be shared with anyone in such a way that the exact analysis can be reproduced. Docker containers can be easily shared through GitHub, thirdparty repositories, or usertouser with plaintext files. Moreover, external tools can hook into Docker directly, using it as a component of complex pipelines or analyses. The Common Workflow Language (CWL) is one specification, which enables researchers to describe analysis tools and workflows that are powerful, easy, and portable. Dynamic computing environments, often referred to as ‘the cloud’, are able to support colocalization of cancer data, Docker+CWL workflows, and the computational resources required to perform largescale analyses. These environments can be extended with collaboration and project management tools to enable researchers to work together in a transparent and reproducible fashion.

These methodologies have enabled globalscale cancer genomics initiatives such as the International Cancer Genome Consortium (ICGC) PanCancer Analysis for Whole Genomes Project (PCAWG), and the National Cancer Institute (NCI) Cancer Genomics Cloud (CGC) pilot program. In this workshop, we will instruct attendees in Docker and CWL as well as their use and best practices, and discuss concretely how these technologies enable scalable, reproducible, and portable cancer informatics. We will also discuss the methodologies behind how these tools are developed and deployed and pose the following questions what are next steps for improving reproducibility in bioinformatics and scale informatics efforts? What have we learned from analyses of thousands of cancer genomes that can be applied to other diseases and other consortium efforts? In addition, we will encourage discussion about unmet needs and future solutions in cancer informatics.

 

Jun
27
12:30 pm12:30

Festival of Genomics Boston Workshop

  • Boston Convention Center

Cancer Genomics at Petabyte Scale: Introduction to the Cancer Genomics Cloud for scalable collaborative, and reproducible analysis of TCGA data and more.

Meeting Homepage

Meeting Summary: The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is one of three pilot systems funded by the national Cancer Institute to explore the paradigm colocalizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them. The CGC makes more than a petabyte of multi-dimensional data available immediately to authorized researchers. In this workshop, participants will gain hands-on experience using the CGC to build and deploy customized analytical workflows to analyze cancer genomics data. Attendees will learn how to use the visual and programmatic interfaces to scale their analyses to hundreds of executions

Jun
3
2:00 pm14:00

Special Seminar: Icahn School of Medicine at Mount Sinai

  • Mt. Sinai: Hess Building Seminar Room A

This seminar will be live-streamed starting at 2pm on Friday June 3rd
GoToMeeting Link: https://global.gotomeeting.com/join/845052117
Meeting ID: 845-052-117
Access Code: 845-052-117

Abstract: CGC hosts The Cancer Genome Atlas (TCGA), one of the world's largest cancer genomics data collections, and provides computational resources and optimized, portable bioinformatics tools to analyze it— at any scale, immediately, collaboratively, and reproducibly. Using Docker and the Common Workflow Language, it is also possible to port any command line tool to the CGC — where researchers have access to free computational credits and more than a petabyte of genomic data to analyze. The CGC project was born out of the recognition that conducting biological research is increasingly computationally-intensive. New approaches are required to support effective data discovery, storage, and computation on large, publicly-funded projects such as TCGA. The CGC is community-focused resource and feedback from researchers will shape its development and ultimately enable us to create the resource that is best suited to needs of the community.

 

May
24
May 25

NCI Cloud Pilot Hands-On Workshop

  • National Cancer Institute

Registration Link

Meeting Summary: The Cancer Genomics Cloud team will be participating in a hands-on workshop designed for those who have a good working knowledge of cancer genomics data, such as contained in The Cancer Genome Atlas (TCGA), and the kinds of analyses performed on this data. Each attendee will have the opportunity to attend half day sessions with two of the three cloud pilots.

May
18
May 20

CWL Technical Hackathon: Tools, Workflows and Workbenches

  • Institut Pasteur

Meeting Homepage

Meeting Summary: The CGC team will be participating in a hackathon focused on tools, pipelines, and the Common Workflow Language at the Institut Pasteur. They'll be working together with developers from the ELIXIR Tools & Data Services Registry, Galaxy, Taverna, Arvados, ReGaTE, and EDAM ontology to promote collaboration and technical developments.

 

May
17
1:00 pm13:00

Webinar: Deploying your own tools on the CGC

Recording of the Webinar

In this webinar, Dr. Gaurav Kaushik will demonstrate how to rapidly and easily bring your own tools to the Cancer Genomics Cloud (CGC) using the Software Development Kit (SDK). With the SDK, any command line tool can be run on the CGC by describing it using the Common Workflow Language. First, we will demonstrate how to use Docker to package a tool so that it can be accessed by the CGC. Then we will demonstrate examples of “wrapping” Linux command line tools and scripts (such as in R). Finally, we will tiptoe into advanced use cases, where you will learn how extend the utility and functionality of your tools to make use of the properties of the TCGA data and metadata on the CGC.

 

May
3
12:00 pm12:00

Weill Cornell Medicine (WCM) Advanced Biomedical Technology Seminar

  • Weill Cornell - Belfer Research Building

Seminar Webpage

We will discuss the motivation, inception, and deployment of the Cancer Genomics Cloud (CGC), built by Seven Bridges and funded by the National Cancer Institute. CGC hosts The Cancer Genome Atlas (TCGA), one of the world's largest cancer genomics data collections, and provides computational resources and optimized, portable bioinformatics tools to analyze it— at any scale, immediately, collaboratively, and reproducibly. Using Docker and the Common Workflow Language, it is also possible to port any tool of your liking to the CGC — where researchers have access to free computational credits and more than a petabyte of genomic data to analyze. The CGC project was born out of the recognition that conducting biological research is increasingly computationally-intensive. New approaches are required to support effective data discovery, storage, and computation on large, publicly-funded projects such as TCGA. The CGC is community driven resource and feedback from researchers will shape its development and ultimately enable us to create the resource that is best suited to needs of the community.

 

Apr
16
Apr 20

American Association for Cancer Research Meeting

  • Ernest N. Morial Convention Center

Meeting Homepage

Meeting Summary: The AACR Annual Meeting is a must-attend event for cancer researchers and the broader cancer community. This year's theme, "Delivering Cures Through Cancer Science," reinforces the inextricable link between research and advances in patient care. The theme will be evident throughout the meeting as the latest, most exciting discoveries are presented in every area of cancer research. There will be a number of presentations that include exciting new data from cutting-edge clinical trials as well as companion presentations that spotlight the science behind the trials and implications for delivering improved care to patients. This cross-cutting, multidisciplinary program will include an outstanding roster of speakers, hundreds of invited talks, and more than 6,000 proffered papers from researchers around the globe. As always, the diversity of the AACR Annual Meeting program will give presenters a forum to share critical updates in all areas, as well as members of the audience an opportunity to actively participate in discussions with colleagues.

Apr
5
Apr 7

Bio-IT World Conference & Expo

  • Seaport World Trade Center

Meeting Homepage

Meeting Summary: Since its debut in 2002, the Annual Bio-IT World Conference & Expo has established itself as a premier event showcasing the myriad of IT and informatics applications and enabling technologies that drive biomedical research, drug discovery & development, and clinical and healthcare initiatives. The Bio-IT World Conference & Expo continues to be a vibrant event that unites 3,000+ life sciences, pharmaceutical, clinical, healthcare, and IT professionals from more than 30 countries. Spanning three days, the 2016 meeting includes 13 parallel conference tracks and 16 pre-conference workshops. Compelling talks, including best practice case studies and joint partner presentations, will feature over 260 of your fellow industry and academic colleagues discussing themes of big data, smart data, cloud computing, trends in IT infrastructure, omics technologies, high-performance computing, data analytics, open source and precision medicine, from the research realm to the clinical arena.

Apr
1
Apr 3

Seven Bridges + NIH BD2K Hackathon

  • Seven Bridges

Meeting Homepage

Meeting Summary: Seven Bridges is proud to announce a hackathon in collaboration with the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. We're inviting the biomedical community to build portable cancer analysis tools to analyze TCGA using the NCI Cancer Genomics Cloud. Seven Bridges is calling on bioinformaticians, data scientists, biomedical researchers, and clinicians of all stripes to collaborate and collectively advance our understanding of cancer and accelerate therapies. If you have a burning question about cancer that you want answered, if you want to use your analytical skills to solve the toughest problems, if you want to learn how to leverage your own research with public data, if you want to contribute to science or the open source community, you want to attend.

Mar
29
1:00 pm13:00

Webinar: Automating analyses on the CGC

Archive link to webinar: https://www.youtube.com/watch?v=spiYwYbeTMY

In this webinar, Dr. Jack DiGiovanna demonstrated how to automate and extend your analyses on the Cancer Genomics Cloud (CGC) using the Application Programming Interface (API). He demonstrated examples of automation (such as launching 100 tasks or application executions in a single method) and extension (such as creating tasks that modify downstream analyses based on intermediary results).

 

Mar
22
1:00 pm13:00

Webinar: Introduction to the CGC

Archive link to the webinar: https://www.youtube.com/watch?v=MOOQ1BFA_JU

In this seminar, Dr. Brandi Davis-Dusenbery highlighted the four guiding principles that have driven development of the Seven Bridges CGC: 

Making data available isn’t enough to make it usable: We’ve built a dynamic query engine that allows fast search of more than 140 clinical and biospecimen properties to enable finding interesting TCGA data faster and easier. Importantly, data are immediately available for analysis at scale using both pre-defined and custom workflows.   

The best science happens in teams: A fine-grained permissions model allows transparent collaboration; in a secure and compliant manner. 

Reproducibility shouldn’t be hard: Each analysis, including all parameters, files, and software versions is fully logged and can be perfectly replicated days or months later. 

The impact of TCGA is amplified by new data and tools: Researchers can readily bring their own data, and their own tools to analyze alongside TCGA data. Native implementation of the Common Workflow Language (CWL) specification enables portability of tools and workflows to and from other CWL-compliant systems. 

The seminar included a demo of the system and interested researchers can visit www.cancergenomicscloud.org to get involved.

Mar
6
Mar 11

Molecular Medicine Tri Conference

  • Moscone North Convention Center

Meeting Homepage

Meeting Summary: Attracting over 3,300 drug discovery and development professionals from over 40 countries in 2015, the Tri-Conference has grown into a diverse event, focusing on Molecular Medicine, specifically on Discovery, Genomics, Diagnostics and Information Technology. With a 23 year history, this year’s expanded coverage includes additional programs on Molecular Diagnostics for Infectious DiseasePrecision Medicineand Cancer Immunotherapy, as well as two new symposia on Companion Diagnostics and the Commercialization of Molecular Diagnostics.

Feb
20
Feb 23

International Symposia of the Association of Biomolecular Resource Facilities (ABRF)

  • 1950 Eisenhower Boulevard Fort Lauderdale, FL 33316

Meeting Homepage

Meeting Summary: The meeting features three main scientific tracks (proteomics, genomics, light microscopy/imaging) and an administrative track (management, professional development and compliance/regulatory issues). We are including an additional track devoted to special sessions that focus on bioinformatics, flow cytometry, monoclonal antibodies and other technologies available through core facilities. Research Groups of ABRF spanning all core technologies will be engaged in developing meeting content, whether by presenting the latest results of studies aimed at gauging the effectiveness of new technologies and methodologies in real laboratory settings, or by hosting scientific session to further emphasize aspects of their technology.

Feb
10
Feb 13

Advances in Genome Biology and Technology

  • JW Marriott Grande Lakes

Meeting Homepage

Meeting Summary: Advances in Genome Biology and Technology (AGBT) General Meeting is our flagship event bringing together technology, software, applications, data resources and public policy. AGBT provides a forum for exchanging information about the latest advances in DNA sequencing technologies, experimental and analytical approaches for genomic studies, and their myriad applications. The meeting format includes daytime plenary sessions that feature invited speakers and abstract-selected talks that highlight cutting-edge research across the broad landscape of genomics. The evening concurrent session includes experimental and computational approaches for effectively utilizing the latest DNA sequencing technologies.

Feb
7
Feb 11

Keystone: The Cancer Genome

  • Fairmont Banff Springs

Visit us at Poster #1021 on Monday, February 8th. 

Meeting Homepage

Meeting Summary: The combination of next-generation sequencing and analysis as applied to experiments studying the cancer genome has revolutionized our understanding of cancer biology. Large-scale cancer genomics has further established a baseline that is now poised to effect the translation of cancer genomics into the clinical setting, effectively transforming patient care. The barriers and challenges to translation are significant, not the least of which involves the transition of research-grade computational and interpretational analysis to clinical-grade analysis. Assays must be highly refined, validated and accurate. How the use of genomic approaches to monitor patient response to therapy, the onset of acquired resistance to therapy and other aspects of patient care will be accepted as a more sensitive partner with conventional imaging approaches must be addressed. Appropriate assignment of therapies to specific gene/protein alterations also will be of paramount importance, especially as the numbers and types of targeted therapies increase. Genomics will also impact our understanding of the immune system's interaction with tumors, leading to the development of personalized vaccine strategies that may provide more durable responses. Specific goals of the meeting include: 1) Providing an overview of computational tools, any gaps in variant detection capabilities and their challenges for clinical implementation; 2) Discussing specific approaches to identify gene-therapy combinations, specifically addressing the difficulty of assessing the impact of DNA mutations on protein function; 3) Identification of the significant efforts ongoing in blood-based ("liquid") biopsy of patients on therapy or following resection surgery; 4) Presentation of current efforts to utilize genomics of individual tumors to inform immunotherapy development; 5) Discussion of efforts at data integration, across "omic" platforms, and also the integration of genomic data with more conventional pathology-based evidence/data. The anticipated outcomes will be the exchange of ideas among international participants on how genomics will impact cancer care and clinical practice and what gaps exist in their existing approaches, as well as development of new collaborations and new enthusiasm for helping to build on the potential of genome-guided approaches to cancer medicine.