KymoMerge: a new tool for analysis of multichannel kymographs

Kymograph analysis is commonly used by researchers to study dynamic processes in cells. Current tools widely available only allow for analysis of one channel kymographs. Here we provide a python-coded, open source program to use as a plug-in for ImageJ which creates one kymograph from the kymographs of two separate channels of one time-lapse movie. This add-in, which we call KymoMerge, therefore allows for analysis of only the co-located tracks in multi-channel movies.

Identifying ZooMS Spectra (mammals) using mMass v1

This is a guide to identifying ZooMS spectra for mammals using the open-source program mMass (Niedermeyer and Strohalm 2012). This guide is intended as a learning tool for students and researchers at the University of Tubingen and is not meant to replace formal ZooMS marker training. If you use this guide to analyse your ZooMS spectra or to convert your data into an open-source format, please cite this document. For further information contact Dr. Samantha Brown (samantha.brown (at) uni-tuebingen.de)

Development of an open source program to identify the size of objects using bright-field microscopy - an automated calibration tool

In light microscopy, eyepiece graticules are commonly used to gauge the size of objects at the micron scale. While this is a relatively simple tool to use, not all microscopes possess this feature. Furthermore, calibrating an eyepiece graticule with a stage micrometer can be time-consuming, particularly for inexperienced microscopists. Similarly, calculating the size of individual objects may also take some time. We present an open-source program to determine the size of objects under a microscope using Python and OpenCV. Taking photos of a stage micrometer under a microscope, we identify gradations on the micrometer and calculate the distance between lines on the micrometer in pixels. From this, we can infer the size of objects from bright-field microscopy images. We believe this will improve access to quantitative microscopy techniques and increase the speed at which samples may be analyzed by light microscopy. Future studies may aim to integrate this with machine learning for object identification

The history of Blitz/Cray-Blitz/Crafty

This article is a series of anecdotes about the development of several programs that advanced the state of the art in computer chess. The best known is Cray Blitz, which won the 1983 and 1986 World Computer Chess Championships. However, in terms of overall impact, perhaps Crafty is the most important. As a high-performing open-source program, it has been used by countless number of researchers and hobbyists to develop computer chess programs for competitions, research, and for fun.

AIMpy: A Python code to solve Schrödinger-like equations with the asymptotic iteration method

This paper presents an open-source program called AIMpy built on Python language. AIMpy is a solver for Schrödinger-like differential equations using asymptotic iteration method (AIM). To confirm that the code works seamlessly, it has been shown through the paper, with recalculation of some previously studied eigenvalue examples, that the code can very well reproduce their results.

Adding Taxonomic Dimensions to the Scientific Names Index in the Biodiversity Heritage Library via Integration with the Catalogue of Life

The most significant specialized and open resource for biodiversity literature is the Biodiversity Heritage Library (BHL). BHL contains more than 200,000 volumes that cover hundreds of years of biological publications. The Catalogue of Life (CoL) is the largest aggregator of global taxonomic information. The Global Names project collaborates with BHL and CoL to create a BHL scientific names index that is continuously improved. The index allows researchers to conveniently find relevant information about any name. Building a scientific names index is challenging because scientific names are quite dynamic and can dramatically change in taxonomic meaning over time. According to our estimates, on average, there are three scientific names per species. Also, a significant number of scientific names have fallen into disuse. For example, approximately 25% of names used in Zoology between 1750–1850 and collected by Charles Sherborn into Index Animalium disappeared from current nomenclatural and taxonomic databases. It is important, therefore, to add "taxonomic intelligence" to BHL names index search and present not only data about a specific name-string but also about all known synonyms so that all relevant information in BHL can be consolidated and conveniently accessed from taxonomic information aggregators like CoL. We developed an open source program "bhlnames", which creates a two-way bridge between the Catalogue of Life and Biodiversity Heritage Library. It provides the location of information in BHL about a taxon, using all names associated with the taxon according to Catalogue of Life synonymy data. Using that information, it attempts to provide CoL with a BHL link to the first descriptions of scientific names in the literature.