Life Sciences Commons^™

Validation Of The Software “Recycling Of Nutrients” In Dairy-Farms Of Western Cuba, I. Rodríguez, Gustavo Crespo, M. F. Días, S. Fraga

IGC Proceedings (1997-2023)

To maintain a good productivity in the soil-plant-animal system it is necessary to achieve an equilibrium between input and output of nutrients and energy. Models and simulation software have been proposed for this purpose. For dairy farms, models have been utilised to show the behaviour of different aspects, such as: feed utilisation, energy flow, digestibility values and daily weight gains (Freer et al., 1970; Assis & France, 1983, Bruce et al., 1984). However, there are few models showing the interaction between soil-plant- animal components of these systems. The objective of the present study was to validate the software …

Software Ppbb_Mx: Potential Productivity Modelling Of Brachiaria Brizantha (Cultivars Marandu And Xaraés), E. R. Detomini, D. Dourado Neto

IGC Proceedings (1997-2023)

Recent improvements in computer capacity and technology allow models to be built to simulate the attributes of many agricultural processes and systems. Although Brachiaria brizantha is the most cultivated tropical grass species in Brazil, there is no single tool to predict its production under optimal conditions. The objective of this paper is to present PPBB_MX software to calibrate and simulate (using a stochastical procedure) the shoot and total biomass potential productivity (output variables) of Brachiaria brizantha as a function of the following input variables: local latitude, season (from cutting date - Julian day), length of regrowth (time, days) and climate …

Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

BACKGROUND: The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.

RESULTS: We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms …

Pyseqrna: An Automated Python Package For Advanced Rna Sequencing Data Analysis And Annotation, Naveen Duhan

Student Research Symposium

Abstract: With the advent of Next-Generation Sequencing (NGS) technologies, numerous data is being generated every day, however, streamlined analysis remains a big hurdle to efficiently use the technology. A large number of algorithms, statistical methods, and software tools have been developed in recent years to perform the individual analysis steps of various NGS applications. Some NGS applications data analysis procedures are therefore very complex, requiring several program tools to be downloaded for their various processing steps. There is a significant room for the development of scalable computing environments that link the individual software components to automated workflows to efficiently and …

The Grazemore Decision Support System To Predict The Quality Of Pasture Grass In Dairy Production, Evelina Larsson

IGC Proceedings (1997-2023)

No abstract provided.

The Grazemore Decision Support System To Optimise Utilisation Of Grazed Grass In Dairy Production, Linda Karlsson

IGC Proceedings (1997-2023)

No abstract provided.

Progress In Grazing Management Of Dairy Cows By Using The Grazemore Dss, Mårten Hetta, Linda Karlsson, Evelina Larsson, Harry Eriksson, Kjell Martinsson

IGC Proceedings (1997-2023)

No abstract provided.

Teaching And Learning Software In Landscape Architecture: A Survey Of Software Use Amongst Faculty And Students, Benjamin H. George, Peter Summerlin, Taz Fulford

Landscape Architecture and Environmental Planning Faculty Publications

Competency in computer software is integral to the profession of landscape architecture, replacing many of the traditional drawing and drafting tools used. This article seeks to capture the current state of software in academia from the perspective of both faculty and students, and to determine if students are achieving the learning levels that faculty are targeting in their courses. Results show that students are attaining faculty’s learning targets, yet students report discontent with the learning process, suggesting that more emphasis is needed to help students understand the role of software in the design process.

Branching Boogaloo: Botanical Adventures In Multi-Mediated Morphologies, Diana Marie Ruggiero

Senior Projects Spring 2016

FormaLeaf is a software interface for exploring leaf morphology using parallel string rewriting grammars called L-systems. Scanned images of dicotyledonous angiosperm leaves removed from plants around Bard’s campus are displayed on the left and analyzed using the computer vision library OpenCV. Morphometrical information and terminological labels are reported in a side-panel. “Slider mode” allows the user to control the structural template and growth parameters of the generated L-system leaf displayed on the right. “Vision mode” shows the input and generated leaves as the computer ‘sees’ them. “Search mode” attempts to automatically produce a formally defined graphical representation of the input …

2matrix: A Utility For Indel Coding And Phylogenetic Matrix Concatenation, Nelson R. Salinas, Damon P. Little

Publications and Research

Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets.

Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs.

Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open …

Upic: Perl Scripts To Determine The Number Of Ssr Markers To Run, R. S. Arias, Linda L. Ballard, Brian E. Scheffler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

We introduce here the concept of Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers. After the first screening of SSR-markers tested on a subset of DNA samples, the user can apply UPIC to find marker combinations that maximize the genetic information obtained by a minimum or desirable number of markers. This allows a cost-effective planning of future experiments. We have developed Perl scripts to calculate all possible subset combinations of SSR markers, and determine based on unique patterns or alleles, which combinations can discriminate among all DNA …

'Paclims': A Component Lim System For High-Throughput Functional Genomic Analysis, Nicole Donofrio, Ravi Rajagopalon, Douglas Brown, Stephen Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas Mitchell, Natalia Galadima, Sara Tucker, Marc J. Orbach, Gayatri Patel, Mark Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee, Ralph A. Dean

Plant Pathology Faculty Publications

BACKGROUND: Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

RESULTS: …