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  • Opus Repository ZIB  (28)
  • 2020-2023  (14)
  • 1990-1994  (14)
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  • 1
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    An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations] (2020)
    Details
    Publication Date: 2020-12-15
    Description: Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
    Language: English
    Type: article , doc-type:article
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    OPUS
  • 2
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    SU(3) Renormalization Group Study on Parallel Computer AP 1000 (1992)
    Details
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 3
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    QCD on the Highly Parallel Computer AP 1000 (1992)
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    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 4
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    On the Difference Between Real and Complex Arrangements. (1991)
    Details
    Publication Date: 2014-02-26
    Description: If $B$ is an arrangement of linear complex Hyperplanes in $C^d$, then the following can be constructed from knowledge of its intersection lattice: (a) the cohomology groups of the complement [Br], (b) the cohomology algebra of the complement [OS], (c) the fundamental group of the complement, if $d\le2$, (d) the singularity link up to homeomorphism, if $d\le3$, (e) the singularity link up to homotopy type [ZZ]. If $B'$ is, more generally, a 2-arrangement in $ R^{2d}$ (an arrangement of real subspaces of codimension 2 with even-dimensional intersections), then the intersection lattice still determines (a) the cohomology groups of the complement [GM] and (e) the homotopy type of the singularity link [ZZ]. We show, however, that for 2-arrangements the data (b), (c) and (d) are not determined by the intersection lattice. They require the knowledge of extra information on sign patterns, which can be computed as determinants of linear relations, or (equivalently) as linking coefficients in the sense of knot theory.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 5
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    Homotopy Types of Subspace Arrangements via Diagrams of Spaces. (1991)
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    Publication Date: 2014-02-26
    Description: We prove combinatorial formulas for the homotopy type of the union of the subspaces in an (affine, compactified affine, spherical or projective) subspace arrangement. From these formulas we derive results of Goresky & MacPherson on the homology of the arrangement and the cohomology of its complement. The union of an arrangement can be interpreted as the direct limit of a diagram of spaces over the intersection poset. A closely related space is obtained by taking the homotopy direct limit of this diagram. Our method consists in constructing a combinatorial model diagram over the same poset, whose homotopy limit can be compared to the original one by usual homotopy comparison results for diagrams of spaces.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 6
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    Coxeter-associahedra. (1993)
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    Publication Date: 2014-02-26
    Description: \def\KPA{\hbox{\rm KPA}}\def\A{{\rm A}}\def\KPW{\hbox{\rm KPW}}\def\W{{\rm W}}\def\B{{\rm B}} \def\D{{\rm D}} Recently M.~M.~Kapranov [Kap] defined a poset $\KPA_{n-1}$, called the {\it permuto-associahedron}, which is a hybrid between the face poset of the permutahedron and the associahedron. Its faces correspond to the partially parenthesized, ordered, partitions of the set $\{1,2,\ldots,n\}$, with a natural partial order. Kapranov showed that $\KPA_{n-1}$ is the face poset of a CW-ball, and explored its connection with a category-theoretic result of MacLane, Drinfeld's work on the Knizhnik-Zamolodchikov equations, and a certain moduli space of curves. He also asked the question of whether this CW-ball can be realized as a convex polytope. We show that this permuto-associahedron corresponds to the type $\A_{n-1}$ in a family of convex polytopes $\KPW$ associated to each of the classical Coxeter groups, $\W = \A_{n-1}, \B_n, \D_n$. The embedding of these polytopes relies on the secondary polytope construction of the associahedron due to Gel'fand, Kapranov, and Zelevinsky. Our proofs yield integral coordinates, with all vertices on a sphere, and include a complete description of the facet-defining inequalities. Also we show that for each $\W$, the dual polytope $\KPW^*$ is a refinement (as a CW-complex) of the Coxeter complex associated to $\W$, and a coarsening of the barycentric subdivision of the Coxeter complex. In the case $\W=\A_{n-1}$, this gives an elementary proof of Kapranov's original sphericity result.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 7
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    Lectures on Polytopes. (1993)
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    Publication Date: 2014-02-26
    Description: These lecture notes have several aims: \begin{itemize} \item to give an introduction to some basic facts about convex polytopes, with an emphasis on the basic methods that yield them (Fourier-Motzkin elimination, Schlegel diagrams, shellability, Gale transforms and oriented matroids), \item to discuss some important examples and elegant constructions (cyclic and neighborly polytopes, zonotopes, Minkowski sums, permutahedra and associahedra, fiber polytopes, the Lawrence construction) \item and to illustrate why polytope theory is exciting, with highlights like Kalai's new diameter bounds, the construction of non-rational polytopes, the Bohne-Dress tiling theorem, shellability and the upper bound theorem, .... \end{itemize} For several of these topics the decisive break-through is very recent, which suggests that there is much more discovered.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
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  • 8
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    Extension Spaces of Oriented Matriods. (1991)
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    Publication Date: 2014-02-26
    Description: We study the space of all extensions of a real hyperplane arrangement by a new pseudo- hyperplane, and, more generally, of an oriented matroid by a new element. The question whether this space has the homotopy type of a sphere is a special case of the "Generalized Baues Problem" of Billera, Kapranov & Sturmfels, via the Bohne-Dress Theorem on zonotopal tilings. We prove that the extension space is spherical for the class of strongly euclidean oriented matroids. This class includes the alternating matroids and all oriented matroids of rank at most 3 or of corank at most 2. In general it is not even known whether the extension space is connected. We show that the subspace of realizable extensions is always connected but not necessarily spherical.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 9
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    A proteomics sample metadata representation for multiomics integration and big data analysis (2021)
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    Publication Date: 2022-02-17
    Description: The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.
    Language: English
    Type: article , doc-type:article
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  • 10
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    Randomized simplex algorithms on Klee-Minty cubes. (1994)
    Details
    Publication Date: 2014-02-26
    Description: We investigate the behavior of randomized simplex algorithms on special linear programs. For this, we develop combinatorial models for the Klee-Minty cubes and similar linear programs with exponential decreasing paths. The analysis of two randomized pivot rules on the Klee-Minty cubes leads to (nearly) quadratic lower bounds for the complexity of linear programming with random pivots. Thus we disprove two bounds conjectured in the literature. At the same time, we establish quadratic upper bounds for random pivots on the linear programs under investigation. This motivates the question whether some randomized pivot rules possibly have quadratic worst-case behavior on general linear programs.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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