Problems. Problem 1. Let Y be a finite type, separated k-scheme. Let E be a locally free OY -module of rank r + 1. Let πE : PY (E)→ Y, φ : π∗E∨ → O(1) be a universal pair of a morphism to Y together with an invertible quotient of the pullback of E∨ (to help calibrate conventions, this is covariant in E with respect to locally split monomorphisms of locally free sheaves). Recall in the proof of ...

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide ...

In this work, we present a short review about the high level design methodology (HLDM), that is based on the use of very high level (VHL) programing language as main, and the use of the intermediate level (IL) language only for the critical processing time. The languages used are Python (VHL) and FORTRAN (IL). Moreover, this methodology, making use of the oriented object programing (OOP), permi...

10 Robust multi-array average (RMA) is a highly successful method for processing raw data from Affymetrix expression microarrays. However, most of the work on microarray data processing predates the widespread use of Python in scientific computing. Here, I describe pyAffy, an efficient implementation of the RMA method in Python/Cython. Using data from the MAQC project, I show that this implemen...

Jit4OpenCL is a new compiler that converts scientific applications written in Python/NumPy into OpenCL code. This compiler is based on unPython, an ahead-of-time compiler from Python/Numpy to an intermediate form and OpenMP code, and on jit4GPU, a just-in-time compiler that converts that intermediate code into AMD CAL code that is specific for AMD GPUs. The targeting of OpenCL provides a new ev...

Direct Numerical Simulations (DNS) of the Navier Stokes equations is a valuable research tool in fluid dynamics, but there are very few publicly available codes and, due to heavy number crunching, codes are usually written in low-level languages. In this work a ~100 line standard scientific Python DNS code is described that nearly matches the performance of pure C for thousands of processors an...

The additional capabilities provided by high-performance neural simulation environments and modern computing hardware has allowed for the modeling of increasingly larger spiking neural networks. This is important for exploring more anatomically detailed networks but the corresponding accumulation in data can make analyzing the results of these simulations difficult. This is further compounded b...

Structured prediction methods have become a central tool for many machine learning applications. While more and more algorithms are developed, only very few implementations are available. PyStruct aims at providing a general purpose implementation of standard structured prediction methods, both for practitioners and as a baseline for researchers. It is written in Python and adapts paradigms and...

This project report attempts to evaluate the educational properties of a relatively new computer language named Python. This is done by examining computer language evolution history, related scientific background work, the existing educational research on computer languages and Python’s experimental application in higher secondary education in Greece, during first half of year 2002. How applica...

Visual secret sharing schemes (VSS) represent an important concept of visual cryptography. They permit the sharing of a secret image between multiple participants so that only authorized groups can recover the secret. This paper considers the software implementation of some black-and-white secret images VSS in Python programming language. PIL (Python Imaging Library) provides strong image proce...