Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Simcluster: clustering enumeration gene expression data on the simplex space

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space.

Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster.

Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data

SILAC-based proteomic quantification of chemoattractant-induced cytoskeleton dynamics on a second to minute timescale

Cytoskeletal dynamics during cell behaviours ranging from endocytosis and exocytosis to cell division and movement is controlled by a complex network of signalling pathways, the full details of which are as yet unresolved. Here we show that SILAC-based proteomic methods can be used to characterize the rapid chemoattractant-induced dynamic changes in the actin–myosin cytoskeleton and regulatory elements on a proteome-wide scale with a second to minute timescale resolution. This approach provides novel insights in the ensemble kinetics of key cytoskeletal constituents and association of known and novel identified binding proteins. We validate the proteomic data by detailed microscopy-based analysis of in vivo translocation dynamics for key signalling factors. This rapid large-scale proteomic approach may be applied to other situations where highly dynamic changes in complex cellular compartments are expected to play a key role

SO/Sp Monopoles and Branes with Orientifold 3 Plane

We study BPS monopoles in 4 dimensional N=4 SO(N) and $Sp(N)$ super Yang-Mills theories realized as the low energy effective theory of $N$ (physical and its mirror) parallel D3 branes and an {\it Orientifold 3 plane} with D1 branes stretched between them in type IIB string theory. Monopoles on D3 branes give the natural understanding by embedding in SU(N) through the constraints on both the asymptotic Higgs field (corresponding to the horizontal positions of D3 branes) and the magnetic charges (corresponding to the number of D1 branes) imposed by the O3 plane. The compatibility conditions of Nahm data for monopoles for these groups can be interpreted very naturally through the D1 branes in the presence of O3 plane.Comment: 18 pages, Latex with RevTex, 1 table, 4 figures, v2: Clarified the introduction and improved on the supersymmetric theory on D1 branes in page 7 and 8 and this final version to appear in Phys.Rev.

One-way multigrid method in electronic structure calculations

We propose a simple and efficient one-way multigrid method for self-consistent electronic structure calculations based on iterative diagonalization. Total energy calculations are performed on several different levels of grids starting from the coarsest grid, with wave functions transferred to each finer level. The only changes compared to a single grid calculation are interpolation and orthonormalization steps outside the original total energy calculation and required only for transferring between grids. This feature results in a minimal amount of code change, and enables us to employ a sophisticated interpolation method and noninteger ratio of grid spacings. Calculations employing a preconditioned conjugate gradient method are presented for two examples, a quantum dot and a charged molecular system. Use of three grid levels with grid spacings 2h, 1.5h, and h decreases the computer time by about a factor of 5 compared to single level calculations.Comment: 10 pages, 2 figures, to appear in Phys. Rev. B, Rapid Communication

Pointlike structure for super p-branes

We present an efficient method to understand the p-brane dynamics in a unified framework. For this purpose, we reformulate the action for super p-branes in the form appropriate to incorporate the pointlike (parton) structure of higher dimensional p-branes and intend to interpret the p-brane dynamics as the collective dynamics of superparticles. In order to examine such a parton picture of super p-branes, we consider various superparticle configurations that can be reduced from super p-branes, especially, a supermembrane, and study the partonic structure of classical p-brane solutions.Comment: 22 pages, corrected typos, to appear in Phys. Rev. D58, 085018 (1998

Quantum Aspects of Supersymmetric Maxwell Chern-Simons Solitons

We study the various quantum aspects of the $N=2$ supersymmetric Maxwell Chern-Simons vortex systems. The fermion zero modes around the vortices will give rise the degenerate states of vortices. We analyze the angular momentum of these zero modes and apply the result to get the supermultiplet structures of the vortex. The leading quantum correction to the mass of the vortex coming from the mode fluctuations is also calculated using various methods depending on the value of the coefficient of the Chern-Simons term $\kappa$ to be zero, infinite and finite, separately. The mass correction is shown to vanish for all cases. Fermion numbers of vortices are also discussed.Comment: 40 pages, ReVTeX, HYUPT-94/04 SNUTP 94-6

ANALISIS BANJIR RANCANGAN DENGAN METODE HSS NAKAYASU PADA BENDUNGAN GINTUNG

Jebolnya Situ Gintung merupakan akibat dari perubahan debit banjir yang terus bertambah. Hal tersebut perlu diana/isis terhadap debit banjir rancangan yang selanjutnya dapat digunakan untuk merencanakan Bendungan Gintung yang baru. Berdasarkan permasalahan di atas, maka perlu dikembangkan perhitungan banjir rancangan dengan metode HSS Nakayasu. Perhitungan dengan menggunaan data hujan. Pada penelitian ini digunakan 18 Pos stasiun penangkar hujan yang diseleksi menurut kelayakan data menjadi 9 pos stasiun hujan dengan memasukan nilai hujan harian maksimum tahunan. Data curah hujan yang disaring memilki tingkat kepercayaan yang rendah, namun masih masuk ke dalam data aman. Dalam penentuan debit banjir rencana terlebih dahulu dilakukan ana/isa frekuensi dan penetapan sebaran data curah hujan kemudian diuji dengan chi-kuadrat. Distribusi yang sesuai adalah distribusi Log Pearson Type III. Dari hasil ana/isa debit banjir rancangan, untuk merencanakan bendungan digunakan debit banjir kala ulang Ql000 = 289,348 m3/dt

Analytic approximations, perturbation methods, and their applications

The paper summarizes the parallel session B3 {\em Analytic approximations, perturbation methods, and their applications} of the GR18 conference. The talks in the session reported notably recent advances in black hole perturbations and post-Newtonian approximations as applied to sources of gravitational waves.Comment: Summary of the B3 parallel session of the GR18 conferenc