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Showing 50 open source projects for "include"
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Jmol
An interactive viewer for three-dimensional chemical structures.
...Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export). -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
...This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss. -
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rRNAFinder
Fast ribosomal RNA detector and annotator
..."rRNAFinder.pl" program included in the package uses nhmmer program searching against the arc.hmm, bac.hmm, and euk.hmm databases to identify rRNA genes from the input contigs. The predicated rRNA genes include 16S, 18S, 23S, 28S, 5S, and 5.8S rRNA genes. The "rna2taxon.pl" program accepts the above generated fasta format rRNA gene sequences as an input to produce the taxonomic assignments for the input genes. The input rRNA gene sequences are searched against the downloaded and reformatted SILVA SSU and LSU databases using blastn. ... -
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The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. ... -
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MPprimer
a program for reliable multiplex PCR primer design
Background: Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. -
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
...FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data. -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A... -
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GNomEx
A Genomic LIMS and Data Repository
...It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy and Agilent Microarrays, Sequenom MassArray and Bioanalyzer. GNomEx is a web application with a Flash client user interface and a Java backend that runs on Apache Tomcat. MySQL is used for the database, although any modern RDBMS can be used. -
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fast_count_multi
Extremely fast NGS read counter
...git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x -
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(NCS) NEQUIM Contact System
Tool for analyze of interactions in ligand-protein complexes
NEQUIM Contact System (NCS) is a system to generate and analyze interaction vectors of protein-ligand complexes. Core features include multiple views of vectors, multiple selection options, cluster analysis and generation of interaction vector model. The input could be from PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex. -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,... -
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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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Drug Extraction
Drug name extraction
...DrugTagger - CRF-based with DrugBank presence feature (see feature set for details). 2. DrugnameGazetteer - gazetteer/dictionary-based. Dictionary created from DrugBank.ca database. Both taggers include grounding/normalisation to DrugBank ids and standard names. Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence feature indicates the presence of the drug name in the DrugBank. Using CONLL-Evaluation: processed 32065 tokens with 3656 phrases; found: 3251 phrases; correct: 2786. ... -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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StatAlign
An extendable statistical multiple alignment tool.
...Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. ... -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
...The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. For each gene the user provides, DEW computes coverage descriptive statistics (RPKM, FKMP and total, mean and median corrected counts), expression profiles (normalized as R/FPKM and trimmed mean of fold change). DEW allows users to explore the data by providing interactive graphs. -
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows users to annotate, for example, draft genome contigs or different genomes concatenated in multi-fasta file in a single step. ... -
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Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
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Tuque
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals -
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven UI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne) etc... ******************************************************************************************************************************** PROJECT MIGRATED TO GITHUB FOR FUTURE UPDATES: https://github.com/biocoder/SBEToolbox/releases ******************************************************************************************************************************** Reference ( In Press ): ================= Konganti K, Wang G, Yang E, Cai JJ* (2013). ... -
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Onco-STS
A web-based Laboratory Information Management System
...The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. The sample tracking system for oncogenomic studies (Onco-STS) is designed to store these data and make them easily accessible to the researchers who work with the samples. ...
