Efficient and Playful Tools to Teach Unix to New Students

Teaching Unix to new students is a common tasks in many higher schools. This paper presents an approach to such course where the students progress autonomously with the help of the teacher. The traditional textbook is complemented with a wiki, and the main thread of the course is a game, in the form of a treasure hunt. The course finishes with a lab exam, where students have to perform practical manipulations similar to the ones performed during the treasure hunt. The exam is graded fully automatically. This paper discusses the motivations and advantages of the approach, and gives an overall view of the tools we developed. The tools are available from the web, and open-source, hence re-usable outside the Ensimag.Comment: ITiCSE, Darmstadt : Germany (2011

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

Study of Tools Interoperability

Interoperability of tools usually refers to a combination of methods and techniques that address the problem of making a collection of tools to work together. In this study we survey different notions that are used in this context: interoperability, interaction and integration. We point out relation between these notions, and how it maps to the interoperability problem. We narrow the problem area to the tools development in academia. Tools developed in such environment have a small basis for development, documentation and maintenance. We scrutinise some of the problems and potential solutions related with tools interoperability in such environment. Moreover, we look at two tools developed in the Formal Methods and Tools group1, and analyse the use of different integration techniques

Ellogon: A New Text Engineering Platform

This paper presents Ellogon, a multi-lingual, cross-platform, general-purpose text engineering environment. Ellogon was designed in order to aid both researchers in natural language processing, as well as companies that produce language engineering systems for the end-user. Ellogon provides a powerful TIPSTER-based infrastructure for managing, storing and exchanging textual data, embedding and managing text processing components as well as visualising textual data and their associated linguistic information. Among its key features are full Unicode support, an extensive multi-lingual graphical user interface, its modular architecture and the reduced hardware requirements.Comment: 7 pages, 9 figures. Will be presented to the Third International Conference on Language Resources and Evaluation - LREC 200

Pando: Personal Volunteer Computing in Browsers

The large penetration and continued growth in ownership of personal electronic devices represents a freely available and largely untapped source of computing power. To leverage those, we present Pando, a new volunteer computing tool based on a declarative concurrent programming model and implemented using JavaScript, WebRTC, and WebSockets. This tool enables a dynamically varying number of failure-prone personal devices contributed by volunteers to parallelize the application of a function on a stream of values, by using the devices' browsers. We show that Pando can provide throughput improvements compared to a single personal device, on a variety of compute-bound applications including animation rendering and image processing. We also show the flexibility of our approach by deploying Pando on personal devices connected over a local network, on Grid5000, a French-wide computing grid in a virtual private network, and seven PlanetLab nodes distributed in a wide area network over Europe.Comment: 14 pages, 12 figures, 2 table

Functional requirements document for the Earth Observing System Data and Information System (EOSDIS) Scientific Computing Facilities (SCF) of the NASA/MSFC Earth Science and Applications Division, 1992

Five scientists at MSFC/ESAD have EOS SCF investigator status. Each SCF has unique tasks which require the establishment of a computing facility dedicated to accomplishing those tasks. A SCF Working Group was established at ESAD with the charter of defining the computing requirements of the individual SCFs and recommending options for meeting these requirements. The primary goal of the working group was to determine which computing needs can be satisfied using either shared resources or separate but compatible resources, and which needs require unique individual resources. The requirements investigated included CPU-intensive vector and scalar processing, visualization, data storage, connectivity, and I/O peripherals. A review of computer industry directions and a market survey of computing hardware provided information regarding important industry standards and candidate computing platforms. It was determined that the total SCF computing requirements might be most effectively met using a hierarchy consisting of shared and individual resources. This hierarchy is composed of five major system types: (1) a supercomputer class vector processor; (2) a high-end scalar multiprocessor workstation; (3) a file server; (4) a few medium- to high-end visualization workstations; and (5) several low- to medium-range personal graphics workstations. Specific recommendations for meeting the needs of each of these types are presented