An object-oriented approach to application generation

The TUBA system consists of a set of integrated tools for the generation of business-oriented applications. Tools and applications have a modular structure, represented by class objects. The article describes the architecture of the environments for file processing, screen handling and report writing

Flexible synthesis of polyfunctionalised 3-fluoropyrroles

An efficient and selective approach for the synthesis of polyfunctionalised 3-fluoropyrroles has been developed starting from commercial aldehydes. The methodology is concise, efficient and allows for the modular and systematic assembly of polysubstituted 3-fluoropyrroles. This synthesis provides an alternative and highly convergent strategy for the generation of these chemically and biologically important units

Additive decompositions for rings of modular forms

We study rings of integral modular forms for congruence subgroups as modules over the ring of integral modular forms for the full modular group. In many cases these modules are free or decompose at least into well-understood pieces. We apply this to characterize which rings of modular forms are Cohen--Macaulay and to prove finite generation results. These theorems are based on decomposition results about vector bundles on the compactified moduli stack of elliptic curves.Comment: Minor changes + new appendix. This article supersedes the algebraic part of arXiv:1609.0926

Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

Additive decompositions for rings of modular forms

We study rings of integral modular forms for congruence subgroups as modules over the ring of integral modular forms for the full modular group. In many cases these modules are free or decompose at least into well-understood pieces. We apply this to characterize which rings of modular forms are Cohen--Macaulay and to prove finite generation results. These theorems are based on decomposition results about vector bundles on the compactified moduli stack of elliptic curves.Comment: Rewritten introduction, updated references. This article supersedes the algebraic part of arXiv:1609.0926

Modular Generation and Customization

Modularity and flexibility can conflict in multi-language systems. For example, the templates commonly used to generate web pages must be manually updated when the database schema changes. Modularity can be improved by generating web pages automatically from the database schema, but it is hard for such a generator to produce the same variety of outputs that are easily achieved by ad hoc edits to a template. Ideally, such ad hoc edits would be abstracted into transformations that compose with the generator, offering both modularity and flexibility. However common customizations cannot be abstracted using the standard techniques of textual identifiers and ordinal positions. These difficulties are distilled into a challenge problem to evaluate potential solutions. A solution is proposed based on field trees, a new data model for software artifacts that provides persistent identifiers and unshifting positions within sequences. But using field trees with conventional programming languages and development environments requires more effort than the ad hoc editing they seek to supplant. Field trees are therefore extended into differential trees, which integrate artifacts and their transformations into a unified representation

On the uniform generation of modular diagrams

In this paper we present an algorithm that generates $k$-noncrossing, $\sigma$-modular diagrams with uniform probability. A diagram is a labeled graph of degree $\le 1$ over $n$ vertices drawn in a horizontal line with arcs $(i,j)$ in the upper half-plane. A $k$-crossing in a diagram is a set of $k$ distinct arcs $(i_1, j_1), (i_2, j_2),\ldots,(i_k, j_k)$ with the property $i_1 < i_2 < \ldots < i_k < j_1 < j_2 < \ldots< j_k$. A diagram without any $k$-crossings is called a $k$-noncrossing diagram and a stack of length $\sigma$ is a maximal sequence $((i,j),(i+1,j-1),\dots,(i+(\sigma-1),j-(\sigma-1)))$. A diagram is $\sigma$-modular if any arc is contained in a stack of length at least $\sigma$. Our algorithm generates after $O(n^k)$ preprocessing time, $k$-noncrossing, $\sigma$-modular diagrams in $O(n)$ time and space complexity.Comment: 21 pages, 7 figure