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]

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

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.

Maxwell Chern-Simons Solitons from Type IIB String Theory

We study various three-dimensional supersymmetric Maxwell Chern-Simons solitons by using type IIB brane configurations. We give a systematic classification of soliton spectra such as topological BPS vortices and nontopological vortices in $\mathcal{N}=2,3$ supersymmetric Maxwell Chern-Simons system via the branes of type IIB string theory. We identify the brane configurations with the soliton spectra of the field theory and obtain a nice agreement with field theory aspects. We also discuss possible brane constructions for BPS domain wall solutions.Comment: 23 pages, Latex, 4 figures; (q_1,q_2)-string convention changed, minor correction

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

N=8 SCFT and M Theory on AdS_4 x RP^7

We study M theory on AdS_4 \times \RP^7 corresponding to 3 dimensional ${\cal N}=8$ superconformal field theory which is the strong coupling limit of 3 dimensional super Yang-Mills theory. For SU(N) theory, a wrapped M5 brane on \RP^5 can be interpreted as baryon vertex. For $SO(N)/Sp(2N)$ theory, by using the property of (co-)homology of \RP^7, we classify various wrapping branes and consider domain walls and the baryon vertex.Comment: 17 pages, Changed baryon like operator as M5 branes in M theory rather than D6 brane in IIA theory. To appear in Phys.Rev.

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

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

X-ray absorption spectroscopy study of diluted magnetic semiconductors: Zn1-xMxSe (M = Mn, Fe, Co) and Zn1-xMnxY (Y = Se, Te)

We have investigated 3d electronic states of doped transition metals in II-VI diluted magnetic semiconductors, Zn1-xMxSe (M = Mn, Fe, Co) and Zn1-xMnxY (Y = Se, Te), using the transition-metal L2,3-edge X-ray absorption spectroscopy (XAS) measurements. In order to explain the XAS spectra, we employed a tetragonal cluster model calculation, which includes not only the full ionic multiplet structure but also configuration interaction (CI). The results show that CI is essential to describe the experimental spectra adequately, indicating the strong hybridization between the transition metal 3d and the ligand p orbitals. In the study of Zn1-xMnxY (Y = Se, Te), we also found considerable spectral change in the Mn L2,3-edge XAS spectra for different ligands, confirming the importance of the hybridization effects in these materials.Comment: This paper consists of 22 pages including 4 figures. This paper is submitted to Physical Review