Life Sciences

iGEM Maya & mMaya tutorials posted

Hi folks,

We've had lots of iGEM teams contact us for information on downloading Autodesk Maya and Digizyme mMaya so far this year.  As you enter the final stretch of getting your presentations ready, we wanted to help you by putting online some great tutorials prepared by our University of Toronto intern, Merry Shiyu Wang.

Click here to find links to all three tutorials on the iGEM site

Here's the first tutorial on getting started with Maya and mMaya.

 

iGEM Team Survey - How's the visualization going?

It's been a ridiculously busy summer continuing to get this project off the ground.  In addition to interviewing around 20 life sciences companies and organizations to gather requirements and feedback on our new effort, we've been hiring and doing a lot more.

One of the facets of our project is to support a variety of academic and professional organizations and get word and information out about Autodesk's current products and their application to Life Sciences tasks.  For the 2nd year in a row, we're supporting the International Genetically Engineered Machine competition (iGEM).  In addition to supporting the growth of the amazing new field of synthetic biology, we've already seen last year's student teams use Autodesk Maya and Digizyme's mMaya to create some fantastic visualizations of their project efforts.

As the competition heats up, we're seeking feedback from the nearly 300 iGEM teams on their efforts with Maya to help tell their story.  Good or bad, we'd like to hear about your experiences. A survey is posted on the main iGEM page and can be found here:

    Autodesk Molecular Visualization Survey for iGEM teams

 

Association of Medical Illustrators 2012 conference wrap up

Saturday night, I returned home after a week in Toronto during which I spent most of my time attending the Association of Medical Illustrators 2012 conference.  The event finished with over 450 attendees, their highest attendance ever (congrats!) and featured an amazing spectrum from incredible fine art to discussions of dinosaurs to fantastic technology advances in visualization.

Some of this year's highlights for me:

Preconference classes: ePMV for me and mMaya for Martin and Merry

There were three of us in attendance who are affiliated with the Autodesk M&E Life Sciences team.  I ended up getting assigned to attend the ePMV course taught by Graham Johnson and Fabian de Kok-Mercad.  Martin and Merry attended the mMaya course, taught by Gaël McGill. Both courses combined a ton of material intended to get medical illustrators jump started with great third party tools that have been specifically designed to help illustrators and animators easily retrieve accurate scientific molecular information from the Protein Data Bank and other sources for display in tools like Autodesk Maya (and Blender and C4D, in the case of ePMV). 

Opening day

The highlights of the opening day fell into two categories for me... academic coolness and amazing futures.  I have a biology and geology background.  I got to see E. O. Wilson present with Gaël McGill about the future of interactive education and their Life on Earth project.  I also got to see Hall Train and Kathryn Chorney present about their experience merging art with science and furthering the process of discovery around paleontology.  Do I need to say more?

In fact, I do. The other part of the first day was the fantastic presentations from 10 student recipients of Vesalius Trust scholarships. The incredibly validating takeaway was that the future of biology lies in games and interaction as modes of education and communication, exactly what we've been proposing here inside Autodesk.  These scholars really presented some awesome work, not least of which was the visualization study done by Merry Wang, our team member for the next few months.

Friday

Friday saw more great talks that filled in the spectrum.  Ben Fry should receive some kind of giant award for what he is doing with Processing. James Gurney presented more dinosaurs... 'nough said.  I was so happy that Bryan Christie summed up by quoting (bad paraphrase warning) "there is nothing new in art" and discussed the fact that technology is just a technique and not the endpoint for fine art.  Graham Johnson also presented about autoCell, his procedural space filling algorithm for cellular environments. (Watch this space for a cool announcement soon.)

Saturday

On Saturday, everyone was back at it, with great presentations from Seth Cooper of the UW FoldIt team, Jeremy Freidberg on game-based education, and the ISO-FORM team on real-time interactive experiences for scientists.  If I needed extra ammunition to say that interaction and gaming are the future, these folks provided it.

A big thanks to everyone we met, especially Linda Wilson-Pauwels who went to extra lengths to make sure we felt included.

Playing with ePMV at AMI 2012

This week, I'm at the Association of Medical Illustrators conference in Toronto, Ontario.  I've gotten to see some great talks already, best amongst them were E. O. Wilson and Gael McGill, Hall Train, and the student talks from the Vesalius Trust scholarship group.  What an impressive look at both some of the foundations of why I entered science to begin with and of what the future looks like.  I hope I can keep up!

One of the fun parts of the week was the generous folks at the University of Toronto Biomedical Communications program who made extra room for Martin Werner and myself to sit in on mMaya and ePMV sessions.  Martin ended up in the Maya session and I ended up watching Graham Johnson and Fabian de Kok-Mercado teach a great session on using ePMV with industry standard 3d modeling tools, such as Autodesk Maya, Cinema 4D, and Blender, to create fantastic images and videos using Protein Data Bank molecular coordinate information.

Here are some of the pieces that I did during (and after) the session.  Great fun to see the artists tools at work.  I don't really do the real artists justice, but some of these images came out cool.

Software developer opening for Autodesk Life Sciences 3D product effort

Hi folks, 

We've opened up a role for a new developer on our Life Sciences team.  We're looking for someone who has familiarity with 3D, life sciences concepts (ideally around Molecular Biology or Chemistry), and if they had multi-platform game development experience, all the better.  The role is going to be based in our 1 Market office in San Francisco.

    Check out and apply for the role here

Have you seen the cool kinds of things our customers produce?  Help us put this capability into the hands of science teams!

Software Developer - Life Sciences

Job Number: 12WD11386

Join a new and growing development team at Autodesk that has the mandate to define, prototype and develop products for the Life and Material Sciences industries, helping scientists from both the industry and academia visualize and simulate their research data.

Building on top of our leading 3D products and technologies, you will work with our subject matter experts and interaction designers to design and implement a solution that will meet the requirements of this new market, focusing on ease of use, high availability as well as on highly specialized and targeted workflows.

 

As a global leader in 3D design, engineering, and entertainment software, Autodesk helps people imagine, design, and create a better world. Autodesk accelerates better design through an unparalleled depth of experience and a broad portfolio of software to give customers the power to solve their design, business, and environmental challenges. In addition to designers, architects, engineers, and media and entertainment professionals, Autodesk helps students, educators, and casual creators unlock their creative ideas through user-friendly applications.

 

Job Title and Number: Software Developer-Life Sciences, #12WD11386

Location: San Francisco, CA; Toronto, Canada or Montreal, Canada

The successful candidate will be a senior software developer with several years of experience in large software development. Experience deploying applications on the cloud and building easy to use interfaces are both assets.

Responsibilities

- Collaborate with other team members to design, prototype and implement the required functionality.
- Work closely with our Web Services team to deliver this functionality as an online cloud offering.
- Deliver well documented code along with extensive unit and automated tests.
- Work closely with the quality assurance group to isolate issues and resolve defects.
- Participate in architecture and code reviews to eliminate implementation problems early in development cycle.

Requirements

- Bachelor degree in Computer Science (or equivalent experience).
- Minimum of 3 years of experience in large scale software development.
- Strong object-oriented skills (such as C++) 
- Experience with the deployment of online applications on the cloud.
- Knowledge of cross-platform application development (Windows, Mac OS and Linux).
- Flexibility and ability to respond quickly to multiple priorities and under changing conditions.
- Good communication skills, both oral and written.

 

Nice to have

- Experience in Life Sciences would be a big plus!

Primary Location

- San Francisco, California

Systems ecology simulations for your body?

One of my geeky dreams since college, if not before, was to create a simulation platform for any kind of ecological discovery.  Population growth, gene migration, resource consumption, foraging, trail construction, you name it.  I always thought that such a system could apply from the microbial level on up.  A great example of an application that showed the value of digital simulation was some interesting work using computer viruses to simulate ecological interaction a few years back... very cool!

Today there seems to be some stir in the news about the Human Microbiome Project, a consortium of commercial and educational agencies that have categorized 10000 various bacteria that live on and inside YOU.

The ecologist in me basically says... how cool is this project!  Mapping out the denizens of the human body, along with geographic and cultural differences, coupled with our ever improving knowledge of protein and metabolic pathways in the body has the opportunity to lead to some incredible opportunities for simulating population behavior and digitally prototyping microbial environments to examine the impacts of drug effects, diseases, and even structural changes to the body.  With about 10x more bacterial cells in your body than human cells, the human symbiotic community organism is incredibly complex and simulation technology continues to offer ways to model and examine how we live, behave, and senesce.

I'm really excited to see how we can link Autodesk visualization and simulation tools into these efforts as our project gets going.

For more information on the Human Microbiome Project check out these links:

• Human Microbiome Project
• Wikipedia description

Leukippos Institute: Open source Synbio in the Cloud

Today I got to chat with a new friend, Gerd Moe-Behrens of the Leukippos Institute.  The Leukippos Institute was founded in 2010 to establish an open source, crowd contributed bioinformatics discovery platform for the synthetic biology domain. Crowd sourced, in silico simulation of synbio creations... very cool!

Given the complexity and diversity of bioinformatics, synbio, and data discovery tools, I can't imagine a better domain for such a platform.  It sounds like this effort would also dovetail nicely into the effort by Boston's Broad Institute to establish an open platform that would funnel bioinformatics output into the clinical diagnostics process.

Check out this Nature blogs interview with Gerd about the plans for Leukippos' apps:

    http://blogs.nature.com/soapboxscience/2012/05/01/tool-tales-leukippos-synthetic-biology-lab-in-the-cloud

Be sure to follow Gerd on twitter at @Socrates_Logos.  He posts some great, relevant articles and is worth following if you are interested in synthetic biology.

 

 

Sr. UX Designer wanted for Life Sciences role

As we get our new Life Sciences effort ramped up, we'll be looking for some new team members.  Here's a role that went live this week on our careers site that we'd love to fill soon!

 

Job Title:  Senior Interaction Designer - Life and Material Sciences  #12WD10942
Location:  San Francisco, CA

Join a new and growing development team at Autodesk that has the mandate to create offerings in emerging scientific markets. These products will help scientists to visualize and simulate their research in industry and academia and will ultimately push the limits of what is possible with computer graphics to see the unseen and predict the unknown.

 

As part of this highly visible team, the Sr. Interaction Designer will conduct field research to understand and determine the needs of these unique customers. S/he will work closely with the Product Manager and development team to translate these customer needs into product requirements and designs.

 

As a global leader in 3D design, engineering, and entertainment software, Autodesk helps people imagine, design, and create a better world. Autodesk accelerates better design through an unparalleled depth of experience and a broad portfolio of software to give customers the power to solve their design, business, and environmental challenges. In addition to designers, architects, engineers, and media and entertainment professionals, Autodesk helps students, educators, and casual creators unlock their creative ideas through user-friendly applications.

 

The successful candidate will be a senior interaction designer with several years of experience in large software development. You must have a strong problem solving abilities and a user centric perspective. Storyboarding workflows and prototyping is important. You must be comfortable designing in new and ambiguous scenarios. The personalities we are looking for are self driven and energetic with the ability to collaborate across disciplines and geographies.

 

You will:

·         Conduct contextual inquiry sessions, task analyses, surveys, and focus groups.

·         Conceptualize, design, and prototype software user interfaces.

·         Plan and conduct usability studies of prototype and development code.

·         Work with technical staff to ensure design integrity during implementation.

 

The right candidate must possess a clear passion for discovering and solving customer problems, a commitment to excellence, and an ability to see beyond the immediate challenges, several years into the future.

 

Required Skills and Experience:

 

-          5+ years in the interaction design field.

-          In-depth knowledge of user-centered design and behavioral sciences.

-          Experience in ethnography, task analysis and persona creation.

-          Experience with relevant design tools (Photoshop, etc.)

-          Experience in planning, conducting and reporting usability tests and site visits.

-          Ability to generate clear product ideas and designs from research findings.

-          Ability to successfully interact with end-users and development team members.

-          Excellent communication skills - written and verbal.

-          At least a Bachelor's degree in design, HCI or a similar field, or 3 years of practical experience.

 

 

Additional Desired Skills (an asset for the role):

 

·         Experience in Life Sciences or Molecular Visualization

·         Knowledge of game design

·         Understanding of 3D modeling

·         Experience designing applications on the cloud.

Incredible DNA robots being designed with the help of Autodesk Maya

60 years ago we didn't know the structure of DNA.

10 years ago we didn't know the nucleotide sequence of human DNA.

5 years ago, Craig Venter's team published the first ever complete sequence of an individual human genome.

Would you believe now that we can fold DNA into 'origami' shapes?

DNA is made up of nucleotides, small molecules containing Carbon, Hydrogen, Nitrogen, and Oxygen, that are linked together to form the long strands that make up the DNA sequence.  A curious behavior of these sequences is that patterns of nucleotides (and sometimes supplementary molecules that are joined to them) can cause the DNA strand to fold and twist.  One manifestation of this behavior is the double helix shape of isolated strands of DNA that is now seen throughout popular culture.

Scientists like Paul W.K. Rothemond discovered that small strands of DNA, when placed near large strands of DNA, can cause the larger strands to fold in predictable shapes.  The technique, called DNA Origami, was originally used to make shapes with little biological significance, such as smiley faces, but the technology involved has the potential to allow researchers to shape complex patterns of DNA that have use in pharmaceuticals, industrial materials, or energy production.

A recent article in the journal Nature discusses the use of DNA Origami to create a 'nanorobot' that was used to deliver a cancer killing agent to cancerous cells.  Such robots are not yet approved for use in humans, but the core science that is making them possible is emerging today.

An intriguing facet of DNA Origami that is interesting for Autodesk is that DNA folding involves complex spatial arrangements of molecules.  One digital tool for creating DNA Origami structures, the open source tool caDNAno created by Shawn Douglas at Harvard, even has the ability to work with Autodesk Maya to create 3D representations of folded DNA structures. 

Take a look at the animation below showing an DNA robot in it's open configuration ready to deliver the drug agent to the cancer cell.

New blog, new domain, new job! Life Sciences and Molecular Visualization at Autodesk

I'm excited to tell you that we're launching a new effort to explore products and technologies for the Life and Molecular Sciences market here at Autodesk.  It's not well known, but a variety of people and organizations have begun using Autodesk products to explore, illustrate, and communicate the complexity and processes that are going on constantly in the living world inside and all around us.

Visual storytelling

We've all seen digital graphics and animation become an accepted component in media from blockbuster games and films to commercials that you see every day on television.  In the architecture and infrastructure world, we have seen the dawn of visual storytelling.  My last product effort was founded on the concept that every planner and engineer wants to be able to convey plans and projects for future infrastructure change to non-technical stakeholders who need 3D and 4D to understand that projects will meet their behavioral and aesthetic requirements.

Life sciences and Autodesk

With life and molecular sciences, we're seeing that scientists, researchers, and educators are intrigued by the potential of the high-end 3D videos that they see on the web and at conferences.  Now they are starting to try to figure out how they can have access to graphically engaging digital media to communicate complex concepts to students, collaborators, and other non-specialist audiences.

Sounds like a perfect fit for Autodesk!

Back to Bio

Personally, I'm thrilled to be back in the biological domain.  Simulating spatial population dynamics with the element of time in 2D is what got my professional career started and it's great that at Autodesk, I've been able to bring the two halves of my career and background back into alignment.  Fast forwarding to 2012, the market offers dramatic opportunity to explore synthetic biology, new forms of educational media, and deepening scientific understanding of life at a time when the average software user is becoming more and more comfortable with 3D and the cloud. 

If you're wondering what some people have already tried with Autodesk solutions, check out this reel of student videos produced for the 2011 iGEM competition, largely with the help of Autodesk Maya and 3rd party tools like the Molecular Maya Toolkit.

This new blog, On the Strand, will help us to communicate some of the events, investigations, and happenings that are going on in the community around us.  There are so many exciting things going on in the life sciences visualization world that you may even find us chatting about trends and technologies that give us some interesting food for thought.

We look forward to exploring this new world with you!