Search Results for "software solution design"
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Showing 39 open source projects for "software solution design"
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. ... -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python source code is available upon request. Milestone:... -
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OligoYap Portable
Oligo design and bioinformatic analysis software.
OligoYap can be used to design classical PCR, SYBR Green, TaqMan, MGB, Molecular Beacons, Microarray and Real-Time PCR primers/probes and for bioinformatics analysis. It has the features of enzyme cut analysis, mutation analysis, DNA/protein match and BLAST. You can easily record laboratory materials/files, prepare PCR mix and many other laboratory operations. It works on windows8.1 and earlier operating systems, but has not been tried on windows10 and later. For better images, you can... -
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
...Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into PhotoShop for rasterization, or used in page design software like Illustrator. -
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CemCon
Automated SMILES-to-optimized 3D molecular structure converter
CemCon is a desktop application developed for automated batch conversion of SMILES strings into optimized 3D molecular structures. The software is designed to simplify ligand preparation workflows for molecular docking, virtual screening, molecular dynamics simulations, and other Computer-Aided Drug Design (CADD) applications. Developed by Abhijit Reang and Sandip Das under the supervision of Dr. Arabinda Ghosh, Department of Molecular Biology and Bioinformatics, Tripura University, India... -
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FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the... -
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packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of sequence analysis tools into a Monte-Carlo algorithm that evolves synthetic sequences towards user-defined goals. -
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rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
...It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. Thanks to its design and implementation, it can be installed on a computation cluster and deployed on an unlimited number of CPUs, allowing HTVS campaigns to be carried out in a matter of days. The rDock program was developed from 1998 to 2006 by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd). ... -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the... -
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We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. ...
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
InMethyl is a Python-based application for the design of target-specific primer combinations for PCR amplification and bisulfite sequencing of complete CpG-islands. InMethyl uses bowtie high-throughoutput aligner to identify potential mis-priming sites in the bisulfite treated or intact genome and then – undesirable potential PCR products. InMethyl provides a balance between various characteristics that allows to pick up primers in hard-to-study genomic regions. -
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MSL
http://dx.doi.org/10.1002/jcc.22968
...Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design). MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories. Reference: Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). ... -
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OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability analysis and elements of experimental design.
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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WebChemViewer
A simple program for sharing molecular structures with associated data
Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. -
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive... -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.
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OptimizeSNP
Selects SNPs and samples with known genotypes for microarray design
Program apply linear programming to minimize the number of microarrays and hybridization experiments that need to be undertaken in order to cover most of the predicted expressed SNPs.Dependencies:. 1) mampl.exe must be in system PATH 2) CPLEX 12.2 must be installed. cplexamp.exe must be in system PATH mampl.exe can be obtained from any program containing AMPL. I obtained AMPL from trial version of MOSEK at http://www.mosek.com/. CPLEX 12.0 can be obtained from... -
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports. -
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Data curation tool to maintain variables for the National Survey of Health and Development managed by the Lifelong Health and Ageing Unit of the Medical Research Council.
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The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.