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Mark Fortner
Works at Aspen Biosciences
Attended Texas A&M
Lives in San Diego, CA
2,654 followers|925,248 views
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Headlines today are heralding a new “simple blood test”, claiming it can predict if a woman will develop breast cancer - but it's too good to be true.
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An interesting JavaScript library for 3D molecular visualization.

3Dmol.js: molecular visualization with WebGL http://bioinformatics.oxfordjournals.org/cgi/content/short/31/8/1322?rss=1
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they do. RCSB PDB will release support for PV shortly.
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Mark Fortner

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Grails 3 Released: Installing Gradle and Groovy 2.4 Support in Eclipse/GGTS http://www.groovyblogs.org/entries/jump?id=24148
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Mark Fortner
owner

Discussion  - 
 
Here's an update to the Linked Open Drug Data. OpenPHACTS and bio2rdf both contain subsets of this data that they aggregate and expose as rdf. What's curious about this, is why this effort is still needed, and why the originating projects aren't providing the data in rdf to begin with.

Granted, the average life scientist probably isn't going to learn sparql to get an answer to his or her question, but that simply begs another question, why don't we have better open source told for querying rdf and visualizing the results?

chem-bla-ics: Linked Open Drug Data: three years on. 
Almost three years ago I collaborated with others in the W3C Health Care and Life Sciences interest group. One of the results of that was a paper in the special issue around the semantic web conference at one of the bianual, ...
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Mark Fortner
owner

Discussion  - 
 
Dr. +Andrew Su 's team at TSRI is hosting a BD2K / NoB hackathon May 7-9th 2015. This 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, hacking on exciting projects, prizes for the best contributions! (1st place: $500 and trophies), and delicious food (provided by Phil's BBQ, Bombay Coast, Regent's Pizza ...)

During this hackathon we will work on projects relating to any of the major challenges of biomedical big data, including:

Locating, gaining access to, standardizing, and documenting data, software tools, and APIs Developing effective, robust, reproducible and interoperable means of sharing data and software tools
Developing new methods for analysing biomedical big data
Training researchers for analysing biomedical big data
For more information see: https://github.com/Network-of-BioThings/nob-hq/wiki/1st-BD2K-3rd-Network-of-BioThings-Hackathon

Register Here: https://www.eventbrite.com/e/bd2k-hackathon-tsri-tickets-16010420599

Add a project idea to the list of projects: https://docs.google.com/document/d/1AEzaMaH1NPBIS9Jg7xVPXbnAs4jlCXbmUk-eUAYkb4k/edit?usp=sharing

We have several scholarships and travel awards available. Please fill out this form to be considered. https://docs.google.com/forms/d/13GqTQ4u43MZSnkaFyXhpg7wO12d-LqH5WgHFxq-1p-o/viewform

Looking forward to seeing you!
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Have him in circles
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I was wondering if a mixture of pancreatic precursor lesions (PanIN, IPMN, MCN) are common in pancreatic cancer patients, or do patients typically have only one type of lesion? +Sally Hodges​
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Thanks +Mark Fortner . Happy to help, but you are correct. Pancreatic cancer is an exceptionally hard nut to crack. However, you know that my dissertation is about epithelial-to-mesenchymal transition and there was a paper recently that demonstrated that the mesenchymal markers in pancreatic cysts predicted worse outcomes (transformation to pancreatic cancer). I asked Anirban Maitra about this, and he concurred that it probably true. You know that he has done considerable research into this also. I think that the key to cysts is the cyst fluid that can be captured at resection. Oddly enough, this is not something that the surgeons at MDACC have been interested in until recently. As you know, when I was at BCM, I was collecting anything that I could get my hands on - cyst fluid, mucin, pancreas juice, whatever.
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“Feed me!” Cancer is caused by the uncontrolled proliferation of cells. Their rapid growth comes with a voracious appetite to support their nutritional demands. To satisfy these demands, cancer cells rewire their metabolism. Increasingly, scientists are looking to exploit the metabolic ...
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More than 50 years ago, the introduction of chemotherapy heralded a new age in the treatment of cancer. Since then and in the past 20 years specifically, cancer researchers have made additional leaps forward in the developmen...
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Mark Fortner
owner

Discussion  - 
 
Some interesting student projects that make use of the OpenPHACTS linked data for drug discovery project.

chem-bla-ics: Programming in the Life Sciences #21: 2014 Screenshots #1. 
December saw the end of this year's PRA3006 course (aka #mcspils). Time to blog some screenshots of the student projects. Like last year, the aim is to use the Open PHACTS API to collect data with ops.js and which should then...
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People
Have him in circles
2,654 people
Panagiotis Alexiou's profile photo
Robert Ladner's profile photo
Himanshu Chuphal's profile photo
Jeff Schnell's profile photo
Ahmed Elsaka's profile photo
Ian Kerr's profile photo
Nathanael Newton's profile photo
Harold Paul's profile photo
Joel Bredeson's profile photo
Education
  • Texas A&M
    Computer Science, 1983 - 1988
Basic Information
Gender
Male
Apps with Google+ Sign-in
Story
Tagline
I write software for scientists.
Introduction
I write code for a living, and in my spare time... I write more code.  Hmm.  Still working on the whole work/life balance thing.  I'm also interested in cancer biology, drug discovery, the semantic web, text mining, Java, JavaFX, Groovy, Grails, NoSQL and all stuff HTML5. 
Bragging rights
Wrote applications to identify drug targets, manage assay data/compounds/screening cascades, identify pathogens in blood, create bioinformatics workflows. Haven't missed a Comic-Con since moving to San Diego.
Work
Occupation
Founder, Principal Consultant
Skills
Java, Groovy, Grails, JavaFX, Swing, XML, JavaScript, HTML5
Employment
  • Aspen Biosciences
    Principal Consultant, 2009 - present
  • Genometrix
    Sr. Software Engineer, 1999 - 2001
  • Lexicon Genetics
    Mgr Bioinformatics, 2001 - 2005
  • Pfizer
    Sr. Analyst, 2006 - 2007
  • L-3 Communcations
    Sr. Software Engineer, 2007 - 2008
  • Takeda Pharmaceuticals
    Sr. Software Engineer, 2008 - 2009
  • Shell Services International
    Consultant, 1997 - 1999
  • University of Houston
    Sr. Bioinformatics Software Engineer, 2005 - 2006
  • Landmark Graphics
    Marketing Technologist, 1994 - 1997
Places
Map of the places this user has livedMap of the places this user has livedMap of the places this user has lived
Currently
San Diego, CA
Previously
Panama City, Panama - Houston, TX - San Diego, CA - Lagos, Nigeria - London, UK - Vienna, Austria - Athens, Greece - Beirut, Lebanon - Clayton, CA
Mark Fortner's +1's are the things they like, agree with, or want to recommend.
Grails And The Semantic Web
www.slideshare.net

In this presentation, we describe the underlying principles of the Semantic Web along with the core concepts and technologies, how they fit

Solar Activity At Birth Could Influence Our Lifespan | IFLScience
www.iflscience.com

While astrology is still a load of rubbish, it turns out that your future could actually be written in the stars after all. Well, star.

Bert Vogelstein’s Liquid Biopsy Blood Test for DNA Could Stop Cancer | M...
www.technologyreview.com

He watched his brother die from a cancer that no drug could cure. Now one of the world’s most renowned cancer researchers says it’s time for

Gmail
mail.google.com

Gmail is email that's intuitive, efficient, and useful. 15 GB of storage, less spam, and mobile access.

New features simplify access to annotation information in NCBI's Gene
www.ncbi.nlm.nih.gov

NCBI NCBI Logo; Skip to main content; Skip to navigation; Resources · All Resources; Chemicals & Bioassays. BioSystems · PubChem BioAssay ·

http://www.the-scientist.com/?articles.view/articleNo/39777/title/Accele...
www.the-scientist.com

Techniques for faster discovery and isolation of human monoclonal antibodies

Increased funding raises hopes in pancreatic cancer research
www.sfgate.com

An uptick in funding for pancreatic cancer research is finally giving scientists some hope that they'll be able to tackle this baffling and

New Cancer Drugs Make Tumors Drug Resistant, More Aggressive
www.ibtimes.com

A popular cancer treatment makes cancer worse, but researchers believe they've found a remedy for that.

Google Calendar
market.android.com

The Calendar app displays events from each of your Google Accounts that synchronizes with your Android device. You can also:- Create, edit,

National Cancer Institute investigating trial outliers to resurrect 'fai...
www.fiercebiotech.com

After sifting through 10 years' worth of clinical trial data, NCI's Cancer Diagnosis Program says the program has identified about 100 "exce

Party drug turned 'miracle' cure for depression spurs hype and stubborn ...
www.fiercebiotech.com

The notion that a party drug could be repurposed into a "miracle" cure for severe, treatment-resistant depression is an almost irresistible

Celgene pays VCs $47M to up its stake in Acceleron's pipeline
www.fiercebiotech.com

The dealmakers at Celgene like to get really, really close to their biotech partners. And nothing demonstrates the sincerity of their intere

Halozyme tanks after another mid-stage setback dings its cancer drug
www.fiercebiotech.com

Halozyme has pressed pause on a Phase II trial of its lead cancer candidate over safety concerns, news that sent the biotech's shares down 2

UPDATED: Pfizer's flagship palbociclib stymies cancer progression but fa...
www.fiercebiotech.com

In the first detailed glimpse of palbociclib's impact on overall survival--a key feature to the future prospects of this flagship program--t

Little Deciphera raises its cancer R&D flag in Boston's bustling...
www.fiercebiotech.com

It's not often you find a little biotech company plugging away at new cancer drugs in out-of-the-way places like Lawrence, KS. But that's ju

Puma surges as neratinib beats Herceptin in head-to-head breast cancer s...
www.fiercebiotech.com

Puma Biotechnology is boasting that its experimental cancer drug neratinib bested Herceptin in a head-to-head study of HER2-positive breast

Lilly preps a PhIII study as breast cancer drug race heats up
www.fiercebiotech.com

One of the big surprises at the annual meeting of the American Association for Cancer Research last weekend belonged to none other than Eli

Challenges for drug development jsr slides aug 2013
www.slideshare.net

MEETING THE CHALLENGES FOR DRUG DEVELOPMENT IN THE 21st CENTURY Jan S. Rosenbaum, Ph.D. CincyTech

A great place for breakfast or that end of the day snack.
Public - a year ago
reviewed a year ago
This hotel needs some help from a decorator. The doors open outward into the hallway, the hallways have Escher-like stairs. The air conditioner is minimal at best. They need to go nonsmoking. Only two TV channels in English and one is RT. The staff makes up for the hotel though, and you're spoiled for choices when it comes to breakfasts. The location is good too. They'll have some stiff competition though when the Motel One Opernring opens up.
Public - a year ago
reviewed a year ago
The food and service is always good at Panera's even at the busiest of times.
Quality: ExcellentAppeal: ExcellentService: Excellent
Public - 2 years ago
reviewed 2 years ago
I've never really figured out what "California Greek" really means, other than as an excuse for inauthenticity, the food and service are always good.
Food: ExcellentDecor: Very GoodService: Excellent
Public - 2 years ago
reviewed 2 years ago
13 reviews
Map
Map
Map
The staff know me by name. Better than most of the banks I've dealt with in the past.
Public - 2 years ago
reviewed 2 years ago
We've been here twice, the food was horrible both times. We won't be back until the Alzheimer's kicks in.
Food: Poor - FairDecor: GoodService: Good
Public - 2 years ago
reviewed 2 years ago
The burger is great, the decor... Not so much. I get that he likes Carlos Santana, but what does that have to do with BBQ?
Food: ExcellentDecor: GoodService: Very Good
Public - 2 years ago
reviewed 2 years ago