prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.
Advancing our understanding of the soil microbial communities using QIIME software: a 16S data analysis pipeline
Rhazya stricta (Apocynaceae) is an important medicinal plant found commonly in South Asia (Pakistan, India and Afghanistan) and the Middle East (i.e. Saudi Arabia, Qatar, United Arab Emirates (UAE), Iran and Iraq). It is used in local folk medicine to treat many diseases such as diabetes mellitus, certain inflammatory conditions, and helminthiasis because leaves of Rhazya stricta contains more than 100 alkaloids with diverse pharmacological properties [1]. Furthermore, as a perennial, it is likely that the associated microflora in the rhizosphere and on the leaves is controlled by the plant itself via these gene products and compounds. Plants use an array of secondary metabolites to defend themselves against harmful organisms and to attract others that are beneficial [2].
Die Populationsdynamik Von Canthocampt Us Staphylinus (Jurine) (Copepoda, Harpacticoida) Im Litoral Des Bodensees
The population dynamics of Canthocamptus staphylinus in the littoral zone of Lake Constance are described (fig. 2). Adult animals aestivate as cysts. The main part of the population emerges from the cysts in autumn. During the resting stage and the first spell after emerging, mortality is very low (fig. 3). Reproduction, expressed as numbers of ovigerous females, begins in November and reaches its maximum in January. The new generation becomes adult in May/June and encysts without previous reproduction. According to Sarvala (1979) it may be possible, that in littoral populations dormancy is induced by long day periods and temperatures of over 12° C (figs. 1, 2). In the profundal zone C. staphylinus also forms cysts, however, both light and temperature are not likely to induce this stage in depths of over 60 m.