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Showing 15 open source projects for "primer"
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System Design Primer
Learn how to design large-scale systems
System Design Primer is a curated, open source collection of resources that helps engineers learn how to design large-scale systems. The project is structured as a comprehensive guide covering core system design concepts, trade-offs, and patterns necessary for building scalable, reliable, and maintainable systems. It offers both theoretical foundations—such as scalability principles, the CAP theorem, and consistency models—and practical exercises, including real-world system design interview questions with sample solutions, diagrams, and code. ... -
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pydna
Clone with Python! Data structures for double stranded DNA
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning. Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways, are often difficult to properly document as is evident from the poor state of documentation in the scientific literature. The pydna python package provide a human-readable formal description of cloning and genetic assembly strategies in Python which... -
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OpenPRED
Herramienta de planificación para redes eléctricas de distribución
...Utiliza las funciones Macros de LibreOffice Basic para desarrollar la lógica del procedimiento, conjuntamente con módulos de software Open Source desarrollados en el marco del proyecto OpenREiD (c) (Software de simulación y optimización de redes eléctricas de distribución), del Instituto de Energía Eléctrica (IEE), UNSJ - CONICET, San Juan - Argentina. Además, integra la herramienta Open Source OpenDSS para el cálculo y simulación de redes de distribución en su versión DLL. Esta primer versión beta permite importar archivos desde DIgSILENT, exportados en formato de planilla de cálculo Excel. -
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OpenPRED-Perú
OpenPRED-Perú es una implementación de OpenPRED para Perú
...Utiliza las funciones Macros de LibreOffice Basic para desarrollar la lógica del procedimiento, conjuntamente con módulos de software Open Source desarrollados en el marco del proyecto OpenREiD (c) (Software de simulación y optimización de redes eléctricas de distribución), del Instituto de Energía Eléctrica (IEE), UNSJ - CONICET, San Juan - Argentina. Además, integra la herramienta Open Source OpenDSS para el cálculo y simulación de redes de distribución en su versión DLL. Esta primer versión beta permite importar archivos desde DIgSILENT, exportados en formato de planilla de cálculo Excel. -
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MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation... -
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InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
...This balance is based on the calculation of scoring factor including primer pair specificity, nucleotide composition (sequence complexity), thermodynamic features (melting temperature, dimers dG etc.), presence of CpG-sites and other parameters. Users are intended to customize the desired or limit ranges of these values, as well as penalties for out-of-bounds values. InMethyl software allows to optimize combination of PCR primer pairs to perform the amplification of large genomic regions, e.g. ... -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
...Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices Package (4) (1) The UniProt Consortium UniProt: a hub for protein information Nucleic Acids Res. 43: D204-D212 (2015). (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013) -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. Both are written to be as lightweight as possible so they can run with minimal memory-requirements on a desktop or laptop as well as on a compute cluster. ... -
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Whois by IP Python
Whois by IP pasandole una archivo de argumento
Uso: Whoisbyip.py <ArchivoLectura> <ArchivoEscritura> Se le pasa como primer parámetro un archivo lleno de IPs (IP por linea) y la salida donde queremos que guarde los diferentes datos recogidos. Realiza una petición whois y busca el campo Country y descr, guardandolo en un archivo.txt separando los datos mediante tabuladores con el objetivo de poder usarlo en excel. -
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Programa escrito en python y que permitira analizar las antenas y tarjetas inalambricas para compararlas asi como calibrar la calidad de la conexion. Este es mi primer programa en python por lo que os ruego comprension.
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Programa escrito en python y que permitira analizar las antenas y tarjetas inalambricas para compararlas asi como calibrar la calidad de la conexion. Este es mi primer programa en python por lo que os ruego comprension.
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Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
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