Allgemein

Vortrag: Fully reproducible and scalable data analysis with Snakemake and Bioconda

Liebe Nutzer,

wir freuen uns am 14. Februar 2017 Dr. Johannes Köster (Centrum Wiskunde & Informatica, Amsterdam und Harvard Medical School) zu Gast zu haben. Er wird um 14:00 Uhr einen Vortrag im Konferenzraum 3 a/b halten "Fully reproducible and scalable data analysis with Snakemake and Bioconda".

Wer sich vorab informieren möchte, kann dies zu snakemake hier tun.

Damit wir Sie über etwaige Änderungen informieren könne und um abzuschätzen, wie stark das Interesse sein wird, bitten wir Sie um einen Eintrag Ihrer Mailadresse.

Die Übertragung von Inhalten aus diesem Formular erfolgt über eine verschlüsselte Verbindung (SSL).

Bitte beachten Sie:

Ihre Mailadresse wird nur verwendet, um Sie über Änderungen bezügliches der Vortragszeit oder des Ortes hinzuweisen und Sie ggf. kurz vorher an den Vortrag zu erinnern.

CAPTCHA ImageBitte nebenstehenden Code hier eingeben. Vielen Dank!
[ Anderes Bild ]

Mit freundlichen Grüßen,
Ihr HPC-Team

Valgrind on Mogon

Dear Developers,

If interested in finding memory leaks or finding cache misses you might heard of the Valgrind Tool Suite . This tool suite can be used on Mogon, too. You can find the relevant documentation (and the reference to the really good Valgrind documentation), here.

Your HPC-Team

Forschungshighlight: Molecular Dynamics on MOGON’s GPU’s

Es ist uns eine Freude Sie auf eine aktuelle Veröffentlichung aus dem Fachbereich Physik hinzuweisen, die durch die Nutzung der GPU-Knoten von MOGON möglich wurde:
"Anomalous Fluctuations of Nematic Order in Solutions of Semiflexible Polymers" von S.A.Egorov, A.Milchev, K.Binder, erschienen inPhysical Review Letters 116, 187801 (2016).
(Alternativ hier)

(a) (a) Snapshot of a system of semiflexible polymers with length N = 32, stiffness \(\epsilon_b = 100 \) , at concentration \(\rho = 0.6 \) (deep in the nematic phase) (b) Typical conformation of a semiflexible polymer in the nematic phase (N = 64, \(\epsilon_b = 16\), \(\rho = 0.4\). (c) Schematic description of nematic order: each chain has its own cylindrical (bent) tube of diameter \(2r_{\rho}\), defined such that it contains only monomers from the considered chain. The tube is placed inside a straight wider cylinder of diameter \(2r_{eff}\). The definition of the deflection length \(\lambda\) is indicated.
(a) Snapshot of a system of semiflexible polymers with length N = 32, stiffness \(\epsilon_b = 100 \) , at concentration \(\rho = 0.6 \) (deep in the nematic phase) (b) Typical conformation of a semiflexible polymer in the nematic phase (N = 64, \(\epsilon_b = 16\), \(\rho = 0.4\). (c) Schematic description of nematic order: each chain has its own cylindrical (bent) tube of diameter \(2r_{\rho}\), defined such that it contains only monomers from the considered chain. The tube is placed inside a straight wider cylinder of diameter \(2r_{eff}\). The definition of the deflection length \(\lambda\) is indicated.
Plot of the deviation from perfect nematic order, \(1-S\), vs the relative reduction \(1 - \langle R^2_e \rangle^{1/2}/L\) of the end-to-end distance for three choices of N = 32, 64, and 128, and three choices of the \(N/\epsilon_b =\) 1, 2, and 4, as indicated. Different points with the same symbol refer to different choices of the density \(\rho\). The fully stretched chain would be the origin of the plot whereas the straight line shows \(1-S = 3\frac{\lambda}{\ell_p}\). Rigid rods would correspond to the ordinate axis here.
Plot of the deviation from perfect nematic order, \(1-S\), vs the relative reduction \(1 - \langle R^2_e \rangle^{1/2}/L\) of the end-to-end distance for three choices of N = 32, 64, and 128, and three choices of the \(N/\epsilon_b =\) 1, 2, and 4, as indicated. Different points with the same symbol refer to different choices of the density \(\rho\). The fully stretched chain would be the origin of the plot whereas the straight line shows \(1-S = 3\frac{\lambda}{\ell_p}\). Rigid rods would correspond to the ordinate axis here.

The nematic ordering in semiflexible polymers with contour length \(L\) exceeding their persistence length \(\ell_{p}\) is described by a confinement of the polymers in a cylinder of radius \(r_{eff}\) much larger than the radius \(r_{\rho}\) expected from the respective concentration of the solution. Large scale Molecular Dynamics simulations combined with Density Functional Theory are used to locate the Isotropic-Nematic \((I−N)\)-transition and to validate this cylindrical confinement. Anomalous fluctuations, due to chain deflections from neighboring chains in the nematic phase are proposed. Considering deflections as collective excitations in the nematically ordered phase of semiflexible polymers elucidates the origins of shortcomings in the description of the \(I−N\) transition by existing theories.

Veröffentlicht am | Veröffentlicht in Allgemein

Carl-Zeiss-Stiftung fördert Kompetenzzentrum für HPC in den Naturwissenschaften in Mainz

Die Carl-Zeiss-Stiftung fördert das Forschungsstrukturkonzept "Kompetenzzentrum für HPC in den Naturwissenschaften" des Instituts für Informatik der Johannes Gutenberg-Universität Mainz (JGU) mit insgesamt 750.000 Euro über vier Jahre. Das geplante Methodenkompetenzzentrum für High Performance Computing (HPC) unter Koordination von Univ.-Prof. Dr. Bertil Schmidt, geschäftsführender Leiter des Instituts für Informatik, und Univ.-Prof. Dr. André Brinkmann, Leiter des Zentrums für Datenverarbeitung (ZDV) der JGU, wird die interdisziplinäre Zusammenarbeit der Naturwissenschaften mit der Informatik an der Johannes Gutenberg-Universität Mainz nachhaltig stimulieren. [mehr]