Milestone M4.3: Simulations interoperable

Milestone M4.3 of work package 4 (SIMEX) in EUCAL

RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are mostly vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN’s capabilities by analyzing a set of 49 Stenotrophomonas maltophilia genomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems across S. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes. RAREFAN is available at http://rarefan.evolbio.mpg.de

Deliverable D4.4 Simulated coherent scattering data from plasma and non–plasma samples

Deliverable D4.4 of work package 4 (SIMEX) in EUCALL

Basics of collaborative research data management: Requirements for a Schleswig-Holstein state initiative on research data management

Das Papier "Grundlagen eines partnerschaftlichen Forschungsdatenmanagements - Anforderungen an eine schleswig-holsteinische Landesinitiative zum Forschungsdatenmanagement" umreißt die Anforderungen für eine schleswig-holsteinische Landesinitiative zum Forschungsdatenmanagement (FDM-SH). Hierfür wird zunächst das Umfeld, in dem eine solche Initiative entstehen und agieren soll, beschrieben. So beeinflussen sowohl die Eigenheiten der regionalen Forschungslandschaft wie auch die Entwicklungen im Bereich der Nationalen Forschungsdateninfrastruktur (NFDI) die Ausprägungen von Landesinitiativen. Die speziellen Anforderungen werden durch den Vergleich mit anderen Landesinitiativen, die Analyse von spezifischen Umfrageergebnissen aus Schleswig-Holstein sowie die Berücksichtigung der Anforderungen der NFDI gesammelt. Der Ansatz des partnerschaftlichen Forschungsdatenmanagements (FDM) spiegelt das Anliegen Schleswig-Holsteins wider, die Herausforderungen für ein zeitgemäßes FDM vor Ort gemeinsam zu bewältigen und dabei sowohl Know-how zu teilen als auch Ressourcen zu schonen

FEL source input for simex_platform tutorial

Simulated x-ray pulse for European XFEL SASE1 beamline 20pC bunch charge (ca. 3 fs pulse duration), undulator length nzc=35, 4.96 keV photon energy. To be used as input file for the simex_platform tutorial on single particle imaging (www.github.com/eucall-software/simex_platform/wiki/SimEx-Tutorial

FELsource 4.96 keV 3fs

<p>XFEL SASE 1 pulses for 4.96 keV photon energy, 20pC bunch charge at undulator length nz=35.</p> <p>Originally queried from https://in.xfel.eu/xpd</p

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

We employ start–to-end simulations to model coherent diffractive imaging of single biomolecules usingx-ray free electron lasers. This technique is expected to yield new structural information about biologically relevantmacromolecules thanks to the ability to study the isolated sample in its natural environment as opposed to crystallizedor cryogenic samples. The effect of the solvent on the diffraction pattern and interpretability of the data is an openquestion. We present first results of calculations where the solvent is taken into account explicitely. They wereperformed with a molecular dynamics scheme for a sample consisting of a protein and a hydration layer of varyingthickness. ThroughR–factor analysis of the simulated diffraction patterns from hydrated samples, we show that thescattering background from realistic hydration layers of up to3 ̊A thickness presents no obstacle for the resolution ofmolecular structures at the sub–nmlevel