Search Results for "sequence scaffold, java"

Triton Inference Server is an open-source inference serving software that streamlines AI inferencing. Triton enables teams to deploy any AI model from multiple deep learning and machine learning frameworks, including TensorRT, TensorFlow, PyTorch, ONNX, OpenVINO, Python, RAPIDS FIL, and more. Triton supports inference across cloud, data center, edge, and embedded devices on NVIDIA GPUs, x86 and ARM CPU, or AWS Inferentia. Triton delivers optimized performance for many query types, including...

...Shell commands, scripts and custom programs can be synchronized inside a single system or in a network of IP connected systems. FLoM supports different types of abstract resources: simple, numeric, set, hierarchical and transactional sequence. libflom, the library shipped with FLoM, allows you to develop your own application using a simple C, C++, Java, Perl, PHP or Python client API. SSL/TLS security for network communication, X.509 certificates for peer to peer mutual authentication.

Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps. (c) Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA. Please...

MSCViewer is a tool intended for debugging of control flows in concurrent, distributed systems. The tool loads logs generated by various entities in the system and visualize a sequence diagram chart for events and interactions. The diagram is fully interactive: entity can be added/removed from the diagram and shuffled; events can be filtered, searched, highlighted and annotated with comments. MSCViewer features integration with a Python interpreter which allows writing Python scripts...

Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation please refer to the link below: https://sourceforge.net/p/ngsscaffolds/wiki/Documentation/

vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu

...It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. ...

nexml is an xml format that represents phylogenetic data (trees, character sequence alignments, sets of OTUs, substitution models). The format is inspired by the commonly used flat-file NEXUS format, but more robust and easier to process.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.

PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

primejobs is program to control and visualize user's commands execution flow. The commands (jobs) are to be executed at specified time in specified sequence. Unlike usual crontab/scripting primejobs allows direct control of the execution flow, setting notifications related to job events, stop/resume execution at any point etc. primejobs design is influenced by OddJob (http://rgordon.co.uk/oddjob/index.html) which is regarded as major breakthrough in understanding how practical job...