Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

Contributions of Vacuum and Plasmon Modes to the Force on a Small Sphere near a Plate

The force on a small sphere with a plasma model dielectric function and in the presence of a perfectly reflecting plane is considered. The contribution of both the vacuum modes of the quantized electromagnetic field and of plasmon modes in the sphere are discussed. In the case that the plasmon modes are in their ground state, quasi-oscillatory terms from the vacuum and plasmon parts cancel one another, leading a monotonic attractive force. If the plasmon modes are not in the ground state, the net force is quasi-oscillatory. In both cases, the sphere behaves in the same way as does an atom in either its ground state or an excited state.Comment: 7 pages, no figures, talk presented at "Quantum Fields under External Conditions - 2005", Barcelona, Spain, September 200

The legitimacy of regulation

I wish to address the topic of property rights and environmental regulation, chiefly the land use regulation that takes place when a rule is made in a plan under the Resource Management Act 1991, the RMA. There has been a lot written on the topic, but mostly by advocates of property rights and critics of regulation. I wish to clear out some of the misconceptions and bring some balance to the debate. My proposition is that it is legal, constitutional, principled, and ethical to regulate the use of land, Land use regulation cannot be dismissed if we are to make progress on amenity, natural character, ecological integrity, biodiversity, and sustainability. Policymakers should remain undeterred by the possibility that RMA regulation will affect the rights of property owners. I will not argue that all land use planning and regulation is done well, nor will I say that they are the only way to solve environmental problems; indeed it would be impossible to agree with either suggestion. I will simply argue that planning and land use regulation have a proper place in the scheme of things

Public Opinion and National Prestige: The Politics of Canadian Army Participation to the Invasion of Sicily, 1942–1943

The participation of Canadian troops in the Sicilian campaign of July and August 1943 marked a distinctive shift in Canada’s war policy, and significantly influenced the employment of the army until the end of hostilities in May 1945. Advocates of Canadian participation in the campaign argued that the overseas army, which had been on garrison duty in Britain since 1939, needed to gain combat experience. Yet it was largely due to political reasons and concerns with prestige rather than military necessity that prompted the Canadian government to bring increasing, and ultimately effective, pressure to bear on the British government to include a Canadian infantry division and tank brigade in Operation “Husky”—the invasion of Sicily

Layer potentials for general linear elliptic systems

In this paper we construct layer potentials for elliptic differential operators using the Lax-Milgram theorem, without recourse to the fundamental solution; this allows layer potentials to be constructed in very general settings. We then generalize several well known properties of layer potentials for harmonic and second order equations, in particular the Green's formula, jump relations, adjoint relations, and Verchota's equivalence between well-posedness of boundary value problems and invertibility of layer potentials.Comment: 20 page

Offshore petroleum and minerals: Plugging gaps in the present framework

For twenty years, it has been realized that there is a gap in New Zealand’s environmental law in that there is no general environmental legislation for the exclusive economic zone, and now for the extended continental shelf that includes areas more than 200 nautical miles offshore. The jurisdiction of regional councils under the Resource Management Act 1991 does not extend beyond the 12-mile limit, about 22 km offshore. (The jurisdiction of territorial authorities extends only to the mean low water mark.) That has meant that oil and gas operations beyond the 12-mile limit have not had proper environmental scrutiny. Public concern about such matters has sharpened in the light of petroleum exploration in the Raukumara Basin off the East Cape, although so far it has only reached the stage of seismic exploration. The Deepwater Horizon blowout on the Macondo prospect in the Gulf of Mexico in April 2010 also looms large in public debate. With a lower profile but with a similar potential to cause environmental harm is the possibility of seabed mining operations. A company is gearing up for deep seabed mining off New Britain in Papua New Guinea. Globally, the main targets are cobalt-rich crusts, polymetallic nodules (on the abyssal plain), and massive sulphide deposits (near hydrothermal vents). In New Zealand iron sands are also attractive. Other possible future uses of the offshore are carbon capture and storage and the extraction of gas hydrates. Existing operations such as fishing by bottom trawling present risks of environmental harm to the benthic environment, especially to features such as seamounts. The Minister for the Environment has now announced his intention to introduce a bill to plug this legal gap, at least in relation to petroleum development and seabed mining. Action on this is most welcome. It is desirable to consider the strengths and weaknesses of the proposal, and of the legal framework for oil and gas well drilling in general. Some surprising gaps remain even if the Minister’s proposal is enacted

A Solvable Toy Model for Tachyon Condensation in String Field Theory

The lump solution of \phi^3 field theory provides a toy model for unstable D-branes of bosonic string theory. The field theory living on this lump is itself a cubic field theory involving a tachyon, two additional scalar fields, and a scalar field continuum. Its action can be written explicitly because the fluctuation spectrum of the lump turns out to be governed by a solvable Schroedinger equation; the \ell=3 case of a series of reflectionless potentials. We study the multiscalar tachyon potential both exactly and in the level expansion, obtaining insight into issues of convergence, branches of the solution space, and the mechanism for removal of states after condensation. In particular we find an interpretation for the puzzling finite domain of definition of string field marginal parameters.Comment: 27 pages, 6 figures, LaTeX. Added references to reflectionless potentials, minor typos correcte