Benjamin J. Bornstein

The systems biology markup language (SBML) : a medium for representation and exchange of biochemical network models

MOTIVATION Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY The specification of SBML Level 1 is freely available from http://www.sbml.org/

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

LibSBML: An API Library for SBML

UNLABELLED LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software. AVAILABILITY LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml.

SBMLToolbox: an SBML toolbox for MATLAB users

SUMMARY We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML. AVAILABILITY SBMLToolbox is freely available from http://sbml.org/software/sbmltoolbox

OASIS: Onboard Autonomous Science Investigation System for Opportunistic Rover Science

The Onboard Autonomous Science Investigation System has been developed to enable a rover to identify and react to serendipitous science opportunities. Using the FIDO rover in the Mars Yard at JPL, we have successfully demonstrated a fully autonomous opportunistic science system. The closed loop system tests included the rover acquiring image data, finding rocks in the image, analyzing rock properties and identifying rocks that merit further investigation. When the system on the rover alerts the rover to take additional measurements of interesting rocks, the planning and scheduling component determines if there are enough resources to meet this additional science data request. The rover is then instructed to either turn toward the rock, or to actually move closer to the rock to take an additional, close-up image. Prototype dust devil and cloud detection algorithms were delivered to an infusion task which refined the algorithms specifically for Mars Exploration Rovers (MER). These algorithms have been integrated into the MER flight software and were recently uploaded to the rovers on Mars.

AEGIS Automated Science Targeting for the MER Opportunity Rover

The Autonomous Exploration for Gathering Increased Science (AEGIS) system enables automated data collection by planetary rovers. AEGIS software was uploaded to the Mars Exploration Rover (MER) mission’s Opportunity rover in December 2009 and has successfully demonstrated automated onboard targeting based on scientist-specified objectives. Prior to AEGIS, images were transmitted from the rover to the operations team on Earth; scientists manually analyzed the images, selected geological targets for the rover’s remote-sensing instruments, and then generated a command sequence to execute the new measurements. AEGIS represents a significant paradigm shift---by using onboard data analysis techniques, the AEGIS software uses scientist input to select high-quality science targets with no human in the loop. This approach allows the rover to autonomously select and sequence targeted observations in an opportunistic fashion, which is particularly applicable for narrow field-of-view instruments (such as the MER Mini-TES spectrometer, the MER Panoramic camera, and the 2011 Mars Science Laboratory (MSL) ChemCam spectrometer). This article provides an overview of the AEGIS automated targeting capability and describes how it is currently being used onboard the MER mission Opportunity rover.

Increased Mars Rover Autonomy using AI Planning, Scheduling and Execution

This paper presents technology for performing autonomous commanding of a planetary rover. Through the use of AI planning, scheduling and execution techniques, the OASIS autonomous science system provides capabilities for the automated generation of a rover activity plan based on science priorities, the handling of opportunistic science, including new science targets identified by onboard data analysis software, other dynamic decision-making such as modifying the rover activity plan in response to problems or other state and resource changes. We first describe some of the particular challenges this work has begun to address and then describe our system approach. Finally, we report on our experience testing this software with a Mars rover prototype.

Autonomous Spectral Discovery and Mapping Onboard the EO-1 Spacecraft

Imaging spectrometers are valuable instruments for space exploration, but their large data volumes limit the number of scenes that can be downlinked. Missions could improve science yield by acquiring surplus images and analyzing them onboard the spacecraft. This onboard analysis could generate surficial maps, summarizing scenes in a bandwidth-efficient manner to indicate data cubes that warrant a complete downlink. Additionally, onboard analysis could detect targets of opportunity and trigger immediate automated follow-up measurements by the spacecraft. Here, we report a first step toward these goals with demonstrations of fully automatic hyperspectral scene analysis, feature discovery, and mapping onboard the Earth Observing One (EO-1) spacecraft. We describe a series of overflights in which the spacecraft analyzes a scene and produces summary maps along with lists of salient features for prioritized downlink. The onboard system uses a superpixel endmember detection approach to identify compositionally distinctive features in each image. This procedure suits the limited computing resources of the EO-1 flight processor. It requires very little advance information about the anticipated spectral features, but the resulting surface composition maps agree well with canonical human interpretations. Identical spacecraft commands detect outlier spectral features in multiple scenarios having different constituents and imaging conditions.

K-means in space: a radiation sensitivity evaluation

Spacecraft increasingly employ onboard data analysis to inform further data collection and prioritization decisions. However, many spacecraft operate in high-radiation environments in which the reliability of dataintensive computation is not known. This paper presents the first study of radiation sensitivity for k-means clustering. Our key findings are 1) k-means data structures differ in sensitivity, which is not determined solely by the amount of memory exposed; 2) no special radiation protection is needed below a data-set-dependent radiation threshold, enabling the use of faster, smaller, and cheaper onboard memory; and 3) subsampling improves radiation tolerance slightly, but the use of kd-trees unfortunately reduces tolerance. Our conclusions can help tailor k-means for use in future high-radiation environments.

Enabling Autonomous Science for a Mars Rover

The Onboard Autonomous Science Investigation System (OASIS) evaluates geologic data gathered by a planetary rover. This analysis is used to prioritize the data for transmission, so that the data with the highest science value is transmitted to Earth. In addition, the onboard analysis results are used to identify and react to new science opportunities. A planning and scheduling component of the system enables the rover to take advantage of identified science opportunities. In this paper, we provide an overview of the OASIS system and report on our experience testing this software with a Mars rover prototype. In particular we discuss how such capabilities can be enabled during ground operations planning and how this increased autonomy will affect downlinked data. We also introduce a new area of OASIS work, which is to provide autonomous targeting capabilities for the MER rovers.