Search results for "Codebase"
showing 3 items of 3 documents
OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data
2021
The Bruker timsTOF Pro is an instrument that couples trapped ion mobility spectrometry (TIMS) to high-resolution time-of-flight (TOF) mass spectrometry (MS). For proteomics, lipidomics, and metabolomics applications, the instrument is typically interfaced with a liquid chromatography (LC) system. The resulting LC-TIMS-MS data sets are, in general, several gigabytes in size and are stored in the proprietary Bruker Tims data format (TDF). The raw data can be accessed using proprietary binaries in C, C++, and Python on Windows and Linux operating systems. Here we introduce a suite of computer programs for data accession, including OpenTIMS, TimsR, and TimsPy. OpenTIMS is a C++ library capable …
Lua Code: Security Overview and Practical Approaches to Static Analysis
2017
Lua is an interpreted, cross-platform, embeddable, performant and low-footprint language. Lua's popularity is on the rise in the last couple of years. Simple design and efficient usage of resources combined with its performance make it attractive for production web applications even to big organizations such as Wikipedia, CloudFlare and GitHub. In addition to this, Lua is one of the preferred choices for programming embedded and IoT devices. This context allows to assume a large and growing Lua codebase yet to be assessed. This growing Lua codebase could be potentially driving production servers and extremely large number of devices, some perhaps with mission-critical function for example i…
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation
2020
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not only makes them challenging to understand and extend, but also difficult to port to other platforms. We present AnySeq - a novel library for computing different types of pairwise alignments of DNA sequences. Our approach combines high performance with an intuitively understandable implementation, which is achieved through the concept of partial evaluation. Using the AnyDSL compiler framework, AnySeq enables the compilation of algorithmic variants that ar…