Search Results for "python" - Page 6
Sort By:
Showing 259 open source projects for "python"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
Forever Free Full-Stack Observability | Grafana CloudBuilt on open standards like Prometheus and OpenTelemetry, Grafana Cloud includes Kubernetes Monitoring, Application Observability, Incident Response, plus the AI-powered Grafana Assistant. Get started with our generous free tier today.
-
1
PolyCTLDesigner
Python scripts for designing polyepitope T-cell immunogens
Given the peptides (T-cell epitopes) PolyCTLDesigner selects flanking sequences to optimize TAP-binding and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing and minimizing the number of junctional epitopes. For constructing polyepitopes PolyCTLDesigner utilizes known amino acid patterns of proteasome cleavage and TAP-binding specificity. PolyCTLDesigner is also able to choose... -
2
Webapp
A web interface to the SnowyOwl gene prediction pipeline
-
3
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/ -
4
ReferenceFree
Scripts for reference free genomic analysis
These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
-
5
ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
6
AMBIENT
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ... -
7
A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
-
8
The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
9
Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
-
Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
-
10
-
11
SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs the following files: .fet.n (feature file) .mask.n (needed for using the new (masked) KlustaKwik) .clu.n (a trivial clue file where everything is put into a single cluster) .fmask.n (trial - float masks instead of binary, we are using this for testing masked KlustaKwik) .spk.n (spike file) .upsk.n (unfiltered spike waveform) .res.n (list of spike times) .xml (an xml file with all the parameters that can subsequently be used by neuroscope or klusters) .fil (highpass filtered data) .h5 ( -
12
Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
-
13
The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
-
14
CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
15
Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
-
16
Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. ... -
17
u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
18
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. -
19
brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
20
GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
-
21
The QIIME project has moved to GitHub. You can now find us at http://github.com/qiime/. As always, you can find the QIIME website at http://www.qiime.org.
-
22
QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
-
23
CancerVaccine
In silico vaccination experiment to determine best vaccination schedul
This project is a simplified representation of the main immune system cells and their interactions. The aim is to simulate the effect of the introduction of a cancer vaccine cell which would stimulate the immune response against the tumor-associated antigen, and consequently against cancer cells themselves. In vivo vaccination experiments take very long to complete, so it would be useful to simulate these experiments such that the best schedule of vaccination is determined that would result... -
24
metaProt
Pipeline to analyze coding regions in metagenomic projects
metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this. -
25
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.
