A Geometric Approach to Molecular Docking and Similarity

We present e cient algorithms coupled to geometric data structures for computation of protein-ligand binding sites (docking) and geometric structure similaritychecks for large biopolymers and siloxane based liquid crystals. Our techniques are novel and based on combinatorial geometry computations of regular triangulations,-shapes and embedded sub-graph isomorphism (matching). While there's a lot more than geometry to the solution of molecular docking and similarity computation problems the approach presented in this paper can be used as the geometric kernel of a more complex methodology including biochemical and energetic considerations

Position Paper: Collaborative Gamification Design for Scientific Software

Gamification, a design trend that is extensively applied to education and citizen science, is regarded as a means to improve scientific software usability. However, development and use of scientific software have special needs and characteristics that might present design challenges. Our position is that gamifi-cation and usability design for scientific software should be facilitated by an open, collaborative design process supported by conversational media. We believe this approach is compatible with qualities often attributed to computational science community re-garding openness and collaboration between members of varied professional backgrounds. Through an illustrative scenario, we ex-emplify the use of conversational media for collaborative design. We expect the synergy between collaborators to result in better us-ability, greater user acceptance, and adequacy to requirements, obtaining optimal design solutions in a sustainable way

The Lens of the Lab: Design Challenges in Scientific Software

Playful and gameful design could improve the quality of scientific software. However, literature about gamification methods for that particular type of software is presently scarce. As an effort to fill that gap, this paper introduces a set of design challenges and opportunities that should be informative to professionals approaching the area. This research is based on literature review on scientific software development, also contemplating material on the gamification of science, software, and work. From the gathered information, we identify, map, and discuss key aspects of development and use of professional scientific software. Those findings are, then, formatted as a Design Lens—a set of questions designers should ask themselves to gain insight, from a particular perspective, on their work. We propose the Lens of the Lab as a design lens to support designers working in collaboration with scientists and software engineers in professional scientific software initiatives

Collaborative Multimedia Scientific Design In SHASTRA

We discuss the application of multimedia in scientific design, and describe a multi-user distributed and collaborative scientific manipulation environment, Shastra, implemented on the multimedia desktop. We highlight salient features of the underlying collaboration infrastructure -- an application conferencing substrate that enables user level cooperation. We demonstrate that, in conjunction with shared contexts, multimedia interfaces -- incorporating text, graphics, audio and video, greatly empowers users in the process of collaborative scientific design