477 research outputs found
The generic mapping tools version 6
The Generic Mapping Tools (GMT) software is ubiquitous in the Earth and ocean sciences. As a cross-platform tool producing high-quality maps and figures, it is used by tens of thousands of scientists around the world. The basic syntax of GMT scripts has evolved very slowly since the 1990s, despite the fact that GMT is generally perceived to have a steep learning curve with many pitfalls for beginners and experienced users alike. Reducing these pitfalls means changing the interface, which would break compatibility with thousands of existing scripts. With the latest GMT version 6, we solve this conundrum by introducing a new "modern mode" to complement the interface used in previous versions, which GMT 6 now calls "classic mode." GMT 6 defaults to classic mode and thus is a recommended upgrade for all GMT 5 users. Nonetheless, new users should take advantage of modern mode to make shorter scripts, quickly access commonly used global data sets, and take full advantage of the new tools to draw subplots, place insets, and create animations.Funding Agency
National Science Foundation (NSF)
Appeared in article as
U.S. National Science Foundation
MSU Geological Sciences Endowmentinfo:eu-repo/semantics/publishedVersio
esys-escript 5.6
Escript is a programming tool for implementing mathematical models in python using the finite element method (FEM). As users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis
esys-escript 5.5
Escript is a programming tool for implementing mathematical models in python using the finite element method (FEM). As users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis
Cleaning up a GNU/Linux operating system
The aim of the thesis is to develop an application for cleaning up the Linux operating system that would be able to function on most distributions. The theoretical part discusses the cleaning of the Linux operating system that frees up disk space and allows a better functioning. The cleaning techniques and the existing tools for Linux are systematically reviewed and presented.
The following part examines the cleaning of the Windows and MacOS operating systems. The thesis also compares all three operation systems and describes the results.
The findings form the basis for our solution. Almost all functionalities work on multiple Linux distributions and the solution is very simple to use. It is also useful on server environments with no graphical interface, as it runs from a terminal. The solution is safe to use because the user can always choose which files to delete before the start of the process, which can also be reversible
biobambam: tools for read pair collation based algorithms on BAM files
Sequence alignment data is often ordered by coordinate (id of the reference
sequence plus position on the sequence where the fragment was mapped) when
stored in BAM files, as this simplifies the extraction of variants between the
mapped data and the reference or of variants within the mapped data. In this
order paired reads are usually separated in the file, which complicates some
other applications like duplicate marking or conversion to the FastQ format
which require to access the full information of the pairs. In this paper we
introduce biobambam, an API for efficient BAM file reading supporting the
efficient collation of alignments by read name without performing a complete
resorting of the input file and some tools based on this API performing tasks
like marking duplicate reads and conversion to the FastQ format. In comparison
with previous approaches to problems involving the collation of alignments by
read name like the BAM to FastQ or duplication marking utilities in the Picard
suite the approach of biobambam can often perform an equivalent task more
efficiently in terms of the required main memory and run-time.Comment: 17 pages, 3 figures, 2 table
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