Category Archives: Genomics News

Newly updated Quick Reference Card

Video Tip of the Week: UCSC Genome Browser in the Cloud (GBIC)

Newly updated Quick Reference CardFor all the years we’ve been out doing training on the UCSC Genome Browser tools, we could watch the evolution of the needs of the researchers and the corresponding features of the UCSC Genome Browser site. At first, people just needed access to the public data. But then they needed ways to add their own data to the public data context and share the views. UCSC gave us custom tracks, and they gave us browser sessions. Woot!

Increasingly, the data sets got bigger and more complex and custom tracks couldn’t handle the volume. UCSC delivered track hubs. Woot!

Some people were telling us that they had patient data that they couldn’t load on to the UCSC site because of privacy and legal issues. Then UCSC delivered GBIB–Genome Browser in a Box. You could download a local copy of the browser and use your own data behind your firewall.

All of these strategies continue to help users combine their own data with the public data and visualize what they want to show. But there’s also another way now–GBIC, Genome Browser in the Cloud. This week’s tip shows you the video the team created to help people to understand what the GBIC can do. There’s additional information about the features that you can see on their announcement, via the mailing list. But just quickly, here’s the nutgraf:

Until now, genomics research groups working with sensitive medical data were largely limited to using local Genome Browser installations to maintain confidentiality, complicating data-sharing among collaborators. Today, the Genome Browser group of the UC Santa Cruz Genomics Institute announced they have changed that by launching a new product, Genome Browser in the Cloud (GBiC). GBiC introduces new freedom to collaborate by allowing rapid Browser installation, in a UNIX-based cloud or UNIX-virtualized cloud.

And here you can have a look at how it works.

In addition, we’ve recently updated our popular Quick Reference Cards, and we added the note that the GBIC can be used to help people work with their own data. You can download those cards, or get some printed ones, from our website. These cards have had to keep evolving over the years to keep up with all the important features that UCSC adds regularly.

Try out the GBIC with your own data. And they are always looking for feedback on how it suits your needs, or other things you might need. Help them evolve.

Disclosure: UCSC Genome Browser tutorials and materials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.

Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Navarro Gonzalez J, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, and Kent WJ. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res. 2016 Nov 29;. PMID: 27899642; PMC: PMC5210591.

OpenHelix to exhibit at TRICON

OpenHelix will be exhibiting at the International Molecular Medicine Tri-Conference (MMTC or TRICON) at booth 129, February 16-18. While onsite at the Tri-Conference, we invite you to demo OpenHelix and not only learn how to enable more effective research, but receive a Starbucks gift card for completing the demo.

The 22nd International Molecular Medicine Tri-Conference is the industry’s Preeminent Event on Molecular Medicine, focusing on Drug Discovery, Genomics, Diagnostics and Information Technology. Spanning six days this year, the Tri-Conference includes an expanded program that includes 6 symposia, over 20 short courses, and 17 conference programs.

OpenHelix provides over 100 tutorial suites on popular and powerful bioinformatics and genomics tools. Each tutorial suites includes 30-60 minute tutorials highlight and explain the features and functionality needed to start using a resource effectively. The tutorial suites also include PowerPoint slides, handouts and exercises to save time and money in teaching others.

An OpenHelix subscription to the tutorials enables quicker and more effective research at your institution through more efficient use of the publicly available tools to access biological data. Join some of the best universities, research institutions, and biotech companies in training scientists on how to use these critical tools.

To schedule your 5 minute demonstration of the OpenHelix site and tutorial suites (and receive a Starbuck’s gift card), email Scott Lathe or call (425) 442-0322. We will be at booth 129 in the Tri-Conference Exhibit Hall.

Oy. I worry about this with cell line studies a lot. Mis-IDed + contaminated.

cellsVia NCBI Announce mailing list:

NCBI BioSample includes curated list of over 400 known misidentified and contaminated cell lines

The NCBI BioSample database now includes a curated list of over 400 known misidentified and contaminated cell lines. Scientists should check this list before they start working with a new cell line to see if that cell line is known to be misidentified.

Continuous cell lines are used widely in research as model systems for normal cellular processes and disease states. However, as noted by many (e.g. PubMed 23235867, 20143388, 19003294, 18072586, and 17522957), cell line cross-contamination or misidentification represents a serious and widespread problem, and researchers should take great care to check that their cell line is what they think it is. Cell lines can be easily mislabeled or become overgrown by cells derived from a different individual, tissue or species.

This problem is so common it is thought that thousands of misleading and potentially erroneous papers have been published using cell lines that are incorrectly identified (PubMed 20448633). The first step in combating this problem is to make sure your cell line is not on the list of known misidentified and cross-contaminated cell lines. Detailed information about how to test your cell lines is provided by the International Cell Line Authentication Committee.

NCBI BioSample curated list of misidentified and contaminated cell lines:[Attribute]

Articles on cell line cross-contamination and misidentification in PubMed mentioned above:

The International Cell Line Authentication Committee:

I also worry about SNV and all sorts of other issues within the cell lines. When the first data was coming out on CNVs in the ENCODE cell lines, I found duplications, and homozygous and heterozygous deletions, that would have concerned me if I was working on certain pathways. If I was still doing cell biology, I’d sequence my cell line of choice before I did another experiment with them.  Below I’ve linked to the PubMed reference they provided in the body.


American Type Culture Collection Standards Development Organization Workgroup ASN-0002. (2010). Cell line misidentification: the beginning of the end, Nature Reviews Cancer, 10 (6) 441-448. DOI:

Cambridge Healthtech Institute Announces the Acquisition of OpenHelix

Cambridge Healthtech Institute (CHI) announced the purchase of Washington–based OpenHelix, the provider of online and onsite training on some of the most popular and powerful open-access bioinformatics resources on the web.

“Knowing how to use the latest bioinformatics tools is critical to genomics research, which will only grow in importance,” said Phillips Kuhl, President of Cambridge Healthtech Institute “With an over ten year track record of developing and presenting training on open access bioinformatics databases and programs, OpenHelix is an instrumental service to researchers and a key addition to CHI’s family of conference and training products.”

OpenHelix will join the Cambridge Healthtech Institute as a division of Bio-IT World, a leading source of news and opinion on technology and strategic innovation in the life sciences, including drug discovery and development. “OpenHelix brings Bio-IT World an extensive and solid audience in the academic research community, as well as the opportunity to extend to our existing audience a valuable training product line,” said Lisa Scimemi, Publisher of Bio-IT World, “training that many of our readers need for themselves or their staff or students but may not be aware of.”

“We are proud of the success we have had in the past, with some of the top universities and medical schools subscribing to OpenHelix,” said Scott Lathe, CEO of OpenHelix “Working with Bio-IT World will bring us the infrastructure, resources, and market reach we need to further grow our tutorials, subscriptions, and product offerings.”

As part of the acquisition, Scott Lathe, CEO and co-founder of OpenHelix will become General Manager of the OpenHelix unit and Mary Mangan, President and co-founder of OpenHelix will become Director, Product and Content of the OpenHelix unit.

About Bio-IT World (
Bio-IT World provides outstanding coverage of cutting-edge trends and technologies that impact the management and analysis of life sciences data, including next-generation sequencing, drug discovery, predictive and systems biology, informatics tools, clinical trials, and personalized medicine. Through a variety of sources including,, Weekly Update Newsletter and the Bio-IT World News Bulletins, Bio-IT World is a leading source of news and opinion on technology and strategic innovation in the life sciences, including drug discovery and development.

About Cambridge Healttech Institute (
Cambridge Healthtech Institute (CHI), founded in 1992, is the industry leader in providing superior-quality scientific information to eminent researchers and business experts from top pharmaceutical, biotech, and academic organizations. Delivering an assortment of resources such as events, reports, publications and eNewsletters, CHI’s portfolio of products include Cambridge Healthtech Institute Conferences, Barnett Educational Services, Insight Pharma Reports, Cambridge Marketing Consultants, Cambridge Meeting Planners, Knowledge Foundation and Cambridge Healthtech Media Group, which includes Bio-IT World and Clinical Informatics News.

About OpenHelix (
OpenHelix, a Washington State company, was founded in 2003 to provide training on what was then a fledgling but quickly growing market of open access web based bioinformatics resources. OpenHelix has provided training and outreach services for many providers of resources, such as the UCSC Genome Browser, OMIM, and the Protein Data Bank (RSCB PDB). OpenHelix received a $1.2 million grant in 2007 to create a search engine for bioinformatics resources and to expand its tutorials suites. In 2009, it launched the subscription service to over 100 tutorial suites.

Public service announcement: Biocuration 2014 meeting

Hi folks–

Got the following email about the upcoming biocuration meeting. You like to have quality information stored in those databases you use? Thank the biocurators. Support the biocurators.


7th International Biocuration Conference
Biocuration 2014
Toronto, Canada
April 6-9, 2014
Abstracts Due: February 10, 2014


Dear Colleagues,

On behalf of the Organizing Committee, I am pleased to invite you to the 7th International Biocuration Conference in Toronto, Canada. The conference will will begin at 6pm on Sunday 6, April and run through to 5pm on Wednesday 9, 2014. The conference will provide a forum for trainees, biocurators, investigators, clinicians and developers of biological databases to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research. Participants from academia, government and industry interested in the methods and tools employed in curation of biological and medical data are encouraged to attend. While a number of speakers have been invited, please note that the majority of oral presentations will be drawn from openly submitted abstracts.

The primary site for the conference is Hart House, considered the cultural and ceremonial centre of the University of Toronto.

The proposed 2014 conference sessions and workshops will address the following challenges in biocuration:

Automated Function Prediction (workshop)
Big Data Curation: Dealing with supplementary data (workshop)
Biocreative Text Mining (workshop)
Biological and Clinical Ontologies (session)
Clinical Annotations (session)
Data Integration and Data Sharing (session)
Functional Annotations (session)
Microbial Informatics (session)
Phenotype (workshop)
Social Tools for publishing and curation (workshop)

Dr. Tim Hubbard, Wellcome Trust Sanger Institute
Dr. Suzanna Lewis, Lawrence Berkeley National Laboratory
Dr. Patricia Babbitt, California Institute for Quantitative Biosciences (QB3)
Dr. Lincoln Stein, Ontario Institute for Cancer Research

The registration form can be found at:

Submit your abstract for presentation (poster or talks only) via this link:

Abstract submission deadline (poster or oral presentation): February 10, 2014
Fellowships Application deadline: February 10, 2014
Notification of decision for abstract submission: February 24, 2014
Fellowships Notification of acceptance: February 24, 2014
Online registration ends: March 24, 2014.

[find this over at the registration site]

Looking forward to seeing you at Biocuration 2014.


Robin Haw

Organizing Committee
Robin Haw (Chair) Ontario Institute for Cancer Research, ON, Canada
Marc Gillespie (Co-chair) St John’s University, NY, USA
Francis Ouellette (Co-chair) Ontario Institute for Cancer Research, ON, Canada
Alex Bateman, European Bioinformatics Institute, UK
Michelle Brazas, Ontario Institute for Cancer Research, ON, Canada
Fiona Brinkman, Simon Fraser University, BC, Canada
Mike Cherry, Stanford University, CA, USA
Patricia Falzon, Ontario Institute for Cancer Research, ON, Canada
Nicole Gleed, Ontario Institute for Cancer Research, ON, Canada
Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland
Iddo Friedberg, Miami University, OH, USA
Todd Harris, Ontario Institute for Cancer Research, ON, Canada
Raja Mazumder, George Washington University, DC, USA
Dennis McCormac, Ontario Genomics Institute, ON, Canada
Ilene Mizrachi, National Center for Biotechnology Information, DC, USA
Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory, CA, USA
John Parkinson, The Hospital for Sick Children, ON, Canada
Paul Thomas, University of California, CA, USA

Boston area genome geeks: free film screening


I posted a short item about that film a few days back, not expecting to hear that there was going to be free access to the screening. I thought it would require conference registration. But it looks like you can see the film without the conference attendance.

For free, I might go.


The Perfect 46. Here we go again.

At least I didn’t say GATTACA, right?

I got an ad today for the Consumer Genetics Conference that had this little teaser, for a “science factual” film.

On September 25 at the Consumer Genetics Conference, a special advance screening of The Perfect 46 will be held. This science factual feature film is about a geneticist who creates a website that pairs individuals with their ideal genetic partner for children. The Perfect 46 hopes to inspire debate about science and our world, specifically the “what ifs?” of personal genetic testing, set in the very near future. The film is without a final sound mix and is still a work in progress. A discussion of the film, the themes it raises, and viewer reactions will be held during an interactive breakout group session the following morning on Thursday, September 26 from 7:30-8:30am. Brett Ryan Bonowicz, the writer and director, will introduce the film and lead the follow-up breakout discussion. > Visit The Perfect 46 Website

Check out the site:

The first item in the FAQ cracked me up:

Q: How does this work?
A: The state of California already has your genome. For a nominal fee, we will run your genome alongside your partner’s genome and address your child’s likelihood for over 4000 genetic diseases.

I get the premise. And maybe this will generate useful discussion. But there are so many ways this could go wrong…We’ll have to see. There are a number of additional short videos/podcasts over on the “press” page for the movie site. I’ll just put one here, from their homepage. But I guess this is the one you should see first.

Hmm. Will this end well? I have been eager to see the genetics-related film “Decoding Annie Parker”. I’m not sure I’m eager for this one.

The Sasquatch Genome paper is out

Um, sorta. I can’t find the sequence in GenBank–ahem.

There’s much chatter right now, but nobody has actually read the paper. I am hoping a qualified science journalist takes a crack at it, because I’m unwilling to pay them (since they bought the journal) to see this thing.

EDIT to add things as they come along:

One person admits to having the paper:

I asked for the sequence accession numbers:

Konrad Karczewski apparently got a copy too, and is tweeting some initial assessment.

This is older:

DNA Day essay contest is open! 60th anniversary of the helix

Got students who are eager to tackle topics in genomics? Got some good science teachers who could coach them? Tell them about the American Society of Human Genetics (ASHG) DNA Day essay contest.

Direct link to the ASHG page in case the tweet one fails:

Over at the site there are more details about the questions to address. And the deadline is noted.


Ethics committee report on genome sequencing and privacy

Well, this changes my morning. It’s a 150 page report.

Get the report itself here: Privacy and Progress in Whole Genome Sequencing

Press or blog coverage (I’ll update if I see others):

Nature: US ethics panel reports on DNA sequencing and privacy

Science: President’s Ethics Panel Urges New Protections for Whole Genome Data

AP: Bioethics panel urges more gene privacy protection

USA Today: Panel: Protect patients who use whole genome sequencing

AARP: How private is your genetic code? Less so than you might think.