Search Results for "python 2"
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Showing 46 open source projects for "python 2"
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Data management solutions for confident marketingVerify, deduplicate, manipulate, and assign records automatically to keep your CRM data accurate, complete, and ready for business.
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Skillfully - The future of skills based hiringSkillfully transforms hiring through AI-powered skill simulations that show you how candidates actually perform before you hire them. Our platform helps companies cut through AI-generated resumes and rehearsed interviews by validating real capabilities in action. Through dynamic job specific simulations and skill-based assessments, companies like Bloomberg and McKinsey have cut screening time by 50% while dramatically improving hire quality.
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Evo 2
Genome modeling and design across all domains of life
Evo 2 is a DNA language model system designed for long-context genome modeling and biological sequence design across all domains of life. The project models DNA at single-nucleotide resolution and supports context windows of up to one million base pairs, which places it in a class of models built for very large genomic reasoning tasks. According to the repository, it uses the StripedHyena 2 architecture, was pretrained with Savanna, and was trained autoregressively on the OpenGenome2 dataset... -
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. ... -
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PDPBioGen
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of the Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author -
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Conscious Artificial Intelligence
It's possible for machines to become self-aware.
This project is a quest for conscious artificial intelligence. A number of prototypes will be developed as the project progresses. This project has 2 subprojects: Object Pascal based CAI NEURAL API - https://github.com/joaopauloschuler/neural-api Python based K-CAI NEURAL API - https://github.com/joaopauloschuler/k-neural-api A video from the first prototype has been made: http://www.youtube.com/watch?v=qH-IQgYy9zg Above video shows a popperian agent collecting mining ore from 3 mining sites and bringing to the base. ... -
Award-Winning Medical Office Software Designed for Your SpecialtyRXNT is an ambulatory healthcare technology pioneer that empowers medical practices and healthcare organizations to succeed and scale through innovative, data-backed, AI-powered software.
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ViReMa
Viral Recombination Mapper
ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. Feb 2014 - Our paper (Open Access) is available at Nucleic Acids Research: "Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data" http://nar.oxfordjournals.org/content/42/2/e11 This is an on-going project and updates will be regularly posted. Please get in touch... -
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HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to... -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods and... -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to... -
Turn traffic into pipeline and prospects into customersDocket is an AI-powered sales enablement platform designed to unify go-to-market (GTM) data through its proprietary Sales Knowledge Lake™ and activate it with intelligent AI agents. The platform helps marketing teams increase pipeline generation by 15% by engaging website visitors in human-like conversations and qualifying leads. For sales teams, Docket improves seller efficiency by 33% by providing instant product knowledge, retrieving collateral, and creating personalized documents. Built for GTM teams, Docket integrates with over 100 tools across the revenue tech stack and offers enterprise-grade security with SOC 2 Type II, GDPR, and ISO 27001 compliance. Customers report improved win rates, shorter sales cycles, and dramatically reduced response times. Docket’s scalable, accurate, and fast AI agents deliver reliable answers with confidence scores, empowering teams to close deals faster.
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This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
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ExSTraCS
Extended Supervised Tracking and Classifying System
...ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ExSTraCS combines a number of recent advancements into a single algorithmic platform. It can flexibly handle (1) discrete or continuous attributes, (2) missing data, (3) balanced or imbalanced datasets, and (4) binary or many classes. A complete users guide for ExSTraCS is included. Coded in Python 2.7. -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). 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 -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
...Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify... -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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Magnolya
De novo CNV detection by co-assembly
Magnolya enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets. -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches... -
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EducationalLCS
eLCS - Educational Learning Classifier System
Educational Learning Classifier System (eLCS) is a set of learning classifier system (LCS) educational demos designed to introduce students or researchers to the basics of a modern Michigan-style LCS algorithm. This eLCS package includes 5 different implementations of a basic LCS algorithm, as part of a 6 stage set of demos that will be paired with the first introductory LCS textbook. Each eLCS implementations (from demo 2 up to demo 6) progressively add major components of the entire... -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
...Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. Multiple mapping reads with a unique location after filtering are rescued and reallocated to the most reliable candidate location. FineSplice requires Python 2.x (>= 2.6) with the following modules installed: pysam (http://code.google.com/p/pysam/) and scikit-learn (http://scikit-learn.org/). For further details check out our publication: Nucl. Acids Res. (2014) doi: 10.1093/nar/gku166 -
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MaryGold
Variation analysis of metagenomic samples
The package enables detection of sequence variation between metagenomic samples. -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are... -
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of... -
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cancer_dynamics
Cancer Dynamics web
Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file. -
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ViAmI-Server
Pattern recognition for ADL events
This software uses computer vision algorithms for mining sequence data from telemonitoring data with CBRs. We propose an approach which treats the detection of changes in behavior detected with a sensor/video fusion, which occur at radically different time-scales, through a CBR in two levels: low and high level. The system is always updating the database with the daily data. -
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NeuroBees
Multi-agent algorithm
Software tool (NEURON, Python, C++) based on the multi-agent Bee algorithm and aiming at multi-parametric optimization. 2 versions : - Link with NEURON (need download and install NEURON and NEURON-python) - Autonomous, with two types of neurones (Izhikevich and hodgkin huxley)
