EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility

A Workflows Roadmap for the Geosciences

The EarthCube Workflows Community Group was formed in March 2012 as part of the NSF EarthCube initiative in response to initial discussions in EarthCube that occurred during 2011. Workflows are used to manage complex computations that have many steps or use large data. Workflow systems assist scientists to select models appropriate for their data, configure them with appropriate parameters, and execute them efficiently. The EarthCube community saw great value in workflow technologies for the future of geosciences. The goal of the EarthCube Workflows Community Group was to begin to elicit requirements for workflows in geosciences, ascertain the state of the art and current practices, identify current gaps in both the use of and capabilities of current workflow systems in the earth sciences through use case studies, and identify grand challenges for the next decade along with the possible paths to addressing those challenges. The group was asked to produce a roadmap for workflows in geosciences. Three other Community Groups were formed (Data, Semantics and Ontologies, and Governance), and each was asked to create a roadmap in their area. The group held a series of virtual and face-to-face workshops to solicit participation from the geosciences community and other relevant researchers. The EarthCube Workflows Community Group set up a public web site where all their activities were made open for participation from the community and all documents were posted for public access and editing (https://sites.google.com/site/earthcubeworkflow/). Presentations and discussions were recorded and posted on the site. A key result of the work of the EarthCube Workflows Community Group activities in Spring and Summer 2012 was the creation of a workflows roadmap for the geosciences. An initial roadmap document for the EarthCube community that was first released in June 2012 and presented to the EarthCube community. A revised roadmap was delivered to the community in August 2012. The roadmap serves as a living document created as a group effort with provisions and a process to update and extend it over time.This document represents the final roadmap of the NSF EarthCube Community Group for workflows in the geosciences. Community feedback is always welcome, as the roadmap will be revised and extended while EarthCube activities continue.This work was supported through National Science Foundation under grant # EAR-1238216 as part of the NSF EarthCube initiative. EarthCube is an innovative and longterm cross-directorate initiative of the US National Science Foundation