Searching, clustering and evaluating biological sequences

The latest generation of biological sequencing technologies have made it possible to generate sequence data faster and cheaper than ever before. The growth of sequence data has been exponential, and so far, has outpaced the rate of improvement of computer speed and capacity. This rate of growth, however, makes analysis of new datasets increasingly difficult, and highlights the need for efficient, scalable and modular software tools. Fortunately most types of analysis of sequence data involve a few fundamental operations. Here we study three such problems, namely searching for local alignments between two sets of sequences, clustering sequences, and evaluating the assemblies made from sequence fragments. We present simple and efficient heuristic algorithms for these problems, as well as open source software tools which implement these algorithms. First, we present approximate seeds; a new type of seed for local alignment search. Approximate seeds are a generalization of exact seeds and spaced seeds, in that they allow for insertions and deletions within the seed. We prove that approximate seeds are completely sensitive. We also show how to efficiently find approximate seeds using a suffix array index of the sequences. Next, we present DNACLUST; a tool for clustering millions of DNA sequence fragments. Although DNACLUST has been primarily made for clustering 16S ribosomal RNA sequences, it can be used for other tasks, such as removing duplicate or near duplicate sequences from a dataset. Finally, we present a framework for comparing (two or more) assemblies built from the same set of reads. Our evaluation requires the set of reads and the assemblies only, and does not require the true genome sequence. Therefore our method can be used in de novo assembly projects, where the true genome is not known. Our score is based on probability theory, and the true genome is expected to obtain the maximum score

Property Claims in GM and Non-GM crops

Conceptualising the ongoing conflict over GM versus non-GM crops in the frame of property rights one can see that economic valorisation dynamics and aspirations are working on both sides, within two differently evolving agri-food paradigms, with biotechnology companies propagating intellectual property rights on seeds and crops within a productivist strategy, and with retailer chains, NGOs, farmer associations claiming generic names and labels as public property rights on identity preserved crops within a consumerist strategy. The analysis shows that the direction and strength of the dynamics depends much on the physical intricacies and the social relations which are implicated in these two types of intangible property. As the development of the intangible property rights lies at the heart of postindustrial knowledge economies, the study of the GM conflict is also instructive for understanding social change in the agri-food sector and in the society more generally

New Techniques for High-Contrast Imaging with ADI: the ACORNS-ADI SEEDS Data Reduction Pipeline

We describe Algorithms for Calibration, Optimized Registration, and Nulling the Star in Angular Differential Imaging (ACORNS-ADI), a new, parallelized software package to reduce high-contrast imaging data, and its application to data from the SEEDS survey. We implement several new algorithms, including a method to register saturated images, a trimmed mean for combining an image sequence that reduces noise by up to ~20%, and a robust and computationally fast method to compute the sensitivity of a high-contrast observation everywhere on the field-of-view without introducing artificial sources. We also include a description of image processing steps to remove electronic artifacts specific to Hawaii2-RG detectors like the one used for SEEDS, and a detailed analysis of the Locally Optimized Combination of Images (LOCI) algorithm commonly used to reduce high-contrast imaging data. ACORNS-ADI is written in python. It is efficient and open-source, and includes several optional features which may improve performance on data from other instruments. ACORNS-ADI requires minimal modification to reduce data from instruments other than HiCIAO. It is freely available for download at www.github.com/t-brandt/acorns-adi under a BSD license.Comment: 15 pages, 9 figures, accepted to ApJ. Replaced with accepted version; mostly minor changes. Software update

Using CamiTK for rapid prototyping of interactive Computer Assisted Medical Intervention applications

Computer Assisted Medical Intervention (CAMI hereafter) is a complex multi-disciplinary field. CAMI research requires the collaboration of experts in several fields as diverse as medicine, computer science, mathematics, instrumentation, signal processing, mechanics, modeling, automatics, optics, etc

Social justice and an information democracy with free and open source software

This paper includes some thoughts on the implications of proprietary software versus free and open source software with regards to social justice, capital, and notions of an information society versus an information democracy. It outlines what free and open source software is and why it is important for social justice, and it offers three cases that highlight two salient themes. This includes a case about preference ordering and decision-making and two cases about knowing and knowledge