Jobs

As we apply for grants to fund more positions, I currently have room in the lab to train/mentor students and interns from around the world, but ideally in the San Francisco Bay area.

In a few cases, if someone with just the right qualifications applies, I may be able to offer a part-time paid position. In the near future I hope to have many full-time paid positions available, so please check back frequently and inquire often.

Looking for project ideas for your masters thesis or undergraduate senior project? Want to dip your toes into the world of molecular animation, molecular visualization, mesoscale modeling, game development, gamification of biology education, database creation or medical illustration?

Here is a small sampling of projects that we need people to work on:

Program a Cytoscape Flux Simulation Engine & Interface to create Interactive Cell Signaling Pathways that Improve Communication and Hypothesis Generation

Apprentices needed for the Fall semester.

Project Description: This project aims to develop new software, sigViz, which researchers can use to create interactive dynamic models of cell signaling pathways that portray accurate structural details for improved communication and hypothesis generation. The tool will serve as an interface for systems biology simulators and by default contains a coarse flux network simulator that non-computational biologists can easily modify or extend. As a Cytoscape plugin, sigViz can natively output simple static and animated graphics, but to impact a broader audience the project will plug into the ubiquitous Python API (uPy) to enable users to create professional quality images and animations driven directly by the interoperating sigViz models. The sigViz app will function in a variety of popular interfaces, including web browsers, to enable researchers from any background to easily access and use the tools with no special training or hardware. To disseminate the software and to encourage a broad community to contribute and curate sigViz models, this project will extend the functionality of an existing database, WikiPathways, to integrate with sigViz and its datatypes rather than directly creating any databases or repositories from scratch. 

Job Description: The student programmer will learn from and work with our team to pare down, clean up, merge and build upon generalized molecular viewer and bioinformatics visualization platforms (including Cytoscape, uPy, ePMV, Chimera, and WikiPathways) currently developed at UCSF and Gladstone, to create sigViz as an intuitive cell signaling visualization and modeling app. 

Qualifications: 1/2 to 1 day per week at UCSF, remaining project hours can be completed remotely. (More time in the lab is better, but this is flexible and negotiable. We can often communicate online during busy periods.) 

Required skills (at least one semester in 2 out of the following 3 programming languages): Java, JavaScript, Python 

Recommended interests (ideal if experienced): Cytoscape programming, 2d/3d animation, graphics software use and graphics programming, HTML and database management, bioinformatics, computational biology 

Weekly Hours: Flexible and negotiable

Related website: http://www.mesoscope.org/projects 
Related website: http://www.sigviz.org



cellPACK Recipe Construction: Establish molecular recipes to build whole 3D cells with full molecular detail using our autoPACK software 

Apprentices needed for the Fall semester. 

Project Description: cellPACK is a specialized version of autoPACK designed to pack biological components together. cellPACK creates 3D models of cell similar to the famous watercolor paintings of David Goodsell: http://mgl.scripps.edu/people/goodsell/illustration/public The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA. We released four recipes that researchers and artists can use to generate models with the initial release of the autoPACK software and cellPACK database. This project will expand that database by providing additional models of subcellular systems as well as entire cells. 

Job Description: A biology or bioinformatics major will do extensive research to populate the database with structural, quantification, and interactome data/annotation for several cellular recipes. They will use the autoPACK software to iteratively test their recipes as they construct 3D models of the systems and will be trained to create web pages, 3D movies, and interactive guided "tours" of the models using the game development platform Unity3D. 

Qualifications: 1/2 to 1 day per week at UCSF, remaining project hours can be completed remotely. (More time in the lab is better, but this is flexible and negotiable. We can often communicate online during busy periods.) 

Required: Biology or Bioinformatics major or similar Or Art major with at least two semesters of biology completed. If you're excited about molecules and cells, we can train you to put them together! 

Recommended interests (ideal if experienced): user experience design, art, illustration, graphic design, molecular biology, structural biology, cell biology, computational biology 

Weekly Hours: 6-9 hrs (Flexible and Negotiable)

Related website: http://www.autopack.org/home 
Related website: http://www.mesoscope.org/projects


autoPACK Algorithm Development: extend the functionality of our open-source 3D packing software (used in molecular/cellular biology, engineering, geology)

Apprentices needed for the Fall semester. 

Project Description: autoPACK is an open-source general packing algorithm that positions 3D objects on surfaces and into/around volumes with zero to minimal overlap depending on the method used and the accuracy vs speed parameters selected by the user. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPACK can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the "loose packing problem" which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) 

Job Description: The student programmer will be offered a selection of modular software components to work on that can extend or improve the functionality of our packing software. Example options include: 
    1. authoring or implementing improved collision detection, signed-distance function, or interaction algorithms 
    2. modifying our referential database and file format architecture or constructing a better approach from scratch. 
    3. Transcribing some of our bottleneck functions from Python into C++ then wrapping the compiles versions in Python for easy access through the autoPACK API 
    4. Incorporating Brownian Dyanamics functions into the resulting models and for use in improving the accuracy of the packing process 
    5. Enhancing the agent behaviors in autoPACK's interaction system to improve packing
    6. Tracking and fixing minor bugs and redesigning massive bottlenecks to improve packing speed 
    7. Parallelizing the packing operations to construct massive models on large computer clusters 
    8. Gamification of the user interface, analysis tools, and outputs, e.g., using Unity3D to provide 3D exploration HUDs directly in browser interfaces (see the website on the gallery) 
    9. Crowd sourcing: Designing a database to display models and collect feedback from biology community experts and the general public alike. 

Qualifications: 1/2 to 1 day per week at UCSF, remaining project hours can be completed remotely. (More time in the lab is better, but this is flexible and negotiable. We can often communicate online during busy periods.) 

Required: Python 

Recommended interests (ideal if experienced): Javascript, C#, C++, HTML, database construction, 3d visualization/graphics, Calculus 3, 2-3 semesters of physics, biology (especially molecular biology), vector and matrix math, game programming, Unity 3D programming, user experience design, art, illustration, graphic design 

Weekly Hours: 6-9 hrs

Related website: http://www.autopack.org/gallery
Related website: http://www.mesoscope.org/projects


Programming Interactive Motor-protein Simulators for Hypothesis-generation, Communication, and Teaching

Apprentices needed for the Fall semester. 

Project Description: The motor-protein simulation software we develop in my visualization lab reduces the labor-intensive protocols required to model and visualize molecular protein motors from protein structure and kinetic data. The software will gather, model, rig, animate and simulate molecular models in order to assemble a series of motor protein model files that follow a new multiscale modeling format under development by the UCSF project mentors. We will further use the files to produce example movies and interactive online “simulators” that will both update the popular, but dated kinesin and muscle myosin animations created by the mentor Johnson for the (Vale and Milligan, Science, 2000) as well as provide new models of all known motor proteins. The online motor protein simulators will allow users to interactively adjust various parameters such as binding and diffusion rates to see the effects on motor proteins, e.g., speed and processivity. The initial simulators will serve as teaching tools, but after integrating more rigorous motor protein walk simulation protocols (e.g., simTK, https://simtk.org/xml/myosin-dynamics.xml) we expect the simulators to become useful thinking models for researchers and foundation models for more detailed simulations. Vale, R.D., and MIlligan, R.A. (2000). The Way Things Move: Looking Under the Hood of Molecular Motor Proteins. Science 288, 88–95. 

Job Description: The student programmer will extend our existing software, a state-machine model that combines brownian dynamics with spatio-temporal decisions based on kinetic rate data, to interoperate with our other 3D visualization systems. They will learn this approach and polish it to recapitulate data of a well characterized molecular motor (conventional kinesin). They will then generalize many of the modular functions to operate on other types of motor proteins. The student can choose to work on interface design where the software will be used both for interactive instruction of biophysics to students of all levels, and as hypothesis generation, mathematical model-> visual model construction, and data analysis tools by researchers. 

Qualifications: 1/2 to 1 day per week at UCSF, remaining project hours can be completed remotely. (More time in the lab is better, but this is flexible and negotiable. We can often communicate online during busy periods.) 

Required: Python programming (at least one semester) 

Recommended interests (ideal if experienced): 3D calculus (matrix and 3D vector math), biology, molecular biology, biophysics, bioinformatics, database, data mining, 3D animation, art, graphic design, user experience design 

Weekly Hours: 6-9 hrs 

Related website: http://www.mesoscope.org/projects
Related website: http://youtu.be/YAva4g3Pk6k
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