Search Results for "pam-python" - Page 25
Sort By:
Showing 2609 open source projects for "pam-python"
View related business solutions-
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.
-
Full-stack observability with actually useful AI | 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
PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
2
PyMathProg
An easy and flexible mathematical programming environment for Python.
PyMathProg is a Python reincarnation of AMPL and GNU MathProg modeling language, implemented in pure Python, connecting to GLPK via swiglpk. Create, optimize, report, change and re-optimize your model with Python, easily integrate database, plotting, etc. -
3
macosx_gpib_lib
Porting of linux-gpib to Mac os x
...The code is mainly based on linux-gpib and includes also code from fxload for mac project. This project generates a dynamic library which can be linked against any kind of application which support dylib. It also comes with a python wrapper. macosx_gpib_lib is not a kernel extension and only supports 82357x adapter for now. It has been designed for 64bits architecture but the target is 10.6. The performance is not as good as linux-gpib is as this library uses Cocoa and not low level functions. -
4
Construct2D
COmputational fluid dyNamics STRUctured grid CreaTor for 2D airfoils
...Elliptic grid generation is still available also. Smooth airfoil surface spacing is handled automatically with user-controlled clustering parameters. Also included is a visualizer written in Python with matplotlib. -
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
5
-
6
IPS Framework
A simple Python framework for loosely-coupled multiphysics simulations
The IPS Framework has migrated to https://github.com/HPC-SimTools/IPS-framework The IPS framework was developed to support loosely-coupled integrated modeling of fusion plasmas (and was originally the Integrated Plasma Simulator). However, the design is quite general, and is suitable for many scientific and engineering domains. In addition to plasma physics, it is also being used in the engineering of batteries. One of the novel features of the IPS framework is its... -
7
chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with... -
8
pySBOL
SWIG-Python wrappers for libSBOL
pySBOL is a SWIG-Python wrapper around libSBOL, a module for reading, writing, and constructing genetic designs according to the standardized specifications of the Synthetic Biology Open Language (SBOL). This page provides binary installers for Windows operating system for Python 2.7 and 3.6. For installation instructions, visit: https://pysbol2.readthedocs.io/en/latest/installation.html For full documentation, visit: https://pysbol2.readthedocs.io/en/latest/index.html -
9
AnyWave is a multi-platform software designed for neurologists and researchers who want to visualise and apply signal processing on electrophysiological signals. AnyWave can handle EEG, SEEG, MEG and more. MATLAB/Python/C++ plugins can be added. See this wiki section to learn how to build AnyWave on Linux : http://meg.univ-amu.fr/wiki/AnyWave:BuildSDK
-
Secure File Transfer for Windows with Cerberus by RedwoodCerberus supports unlimited users and connections on a single IP, with built-in encryption, 2FA, and a browser-based web client — all deployable in under 15 minutes with a 25-day free trial.
-
10
Inelastica
Transport code and tools based on SIESTA and TranSIESTA (DFT-NEGF)
...Pre- and post-processing tools for SIESTA (DFT, quantum chemistry) and TranSIESTA (quantum transport): (1) Calculate phonon frequencies, e-ph couplings, and inelastic contributions to the conductance (IETS). (2) Access Hamiltonian etc from Python. Some code documentation and installation instructions are available at this mediawiki page: http://dipc.ehu.es/frederiksen/inelastica/index.php. -
11
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/ -
12
Acoustic Research Tool (ART)
Acoustic Simulation Library for Frequency and Time Domain Simulations.
ART is a flexible simulation framework for wind instruments. It includes a growing library of modelling elements. So far bore discontinuities, branches, tone holes, cylindrical and conical tubes, Bessel horns and bent tubes are available for frequency domain modelling. In the time domain generic bidirectional propagation elements, scattering elements, fractional delays, convolution with reflection functions and general z-domain networks are available and can be described using MuParserX... -
13
trnsys-fmu
The FMI++ TRNSYS FMU Export Utility
This project has been moved to https://github.com/fmipp/trnsys-fmu This open-source project provides a stand-alone tool for exporting FMUs for Co-Simulation from TRNSYS 17 models. The current release supports FMI version 1.0 and 2.0. Instructions on installation and usage are given in the documentation, which is provided as part of the download. This documentation also contains a tutorial on how to export a TRNSYS model as FMU for co-simulation and how to link it with a simple... -
14
DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
This project contains Python scripts usable for a dual transcript-discovery approach that improves the delimitation of gene features from RNA-seq data in the chicken model. Documentation: http://bio.biologists.org/content/biolopen/suppl/2018/01/17/bio.028498.DC1/BIO028498supp.pdf Citation: Orgeur M., Martens M., Börno S. T., Timmermann B., Duprez D. and Stricker S. (2018). -
15
Mixture100
Simply percent calculator
For making various mixtures, like homemade alcohol, brine or e-liquids. Add a components, set a percentage in total, set how much I want a given mixture and save, share or print recipe. -
16
TekDS820
Drive your obsolete Tek oscilloscope remotely with python
Control a Tek TDS-820 remotely via a GPIB interface using linux-gpib, python, matplotlib and tkinter. The programming manual is used to generate an XML schema which is then used to assist in building extra functionality into the tkinter user interface. -
17
ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
-
18
Morinus
Exquisite Astrology Software
Astrology software for all. -
19
NOTE: the project has moved to https://scipy.org/scipylib/ --- go there to find latest versions. This sourceforge project contains only old historical versions of the software. SciPy is package of tools for science and engineering for Python. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more.
-
20
pyCGNS
A Python package for CGNS
pyCGNS is now on github: https://pycgns.github.io/index.html https://github.com/pyCGNS/pyCGNS -
21
AI learning
AiLearning, data analysis plus machine learning practice
We actively respond to the Research Open Source Initiative (DOCX) . Open source today is not just open source, but datasets, models, tutorials, and experimental records. We are also exploring other categories of open source solutions and protocols. I hope you will understand this initiative, combine this initiative with your own interests, and do what you can. Everyone's tiny contributions, together, are the entire open source ecosystem. We are iBooker, a large open-source community,... -
22
Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
-
23
Spectral-SpecPro
Spectral - software for manipulating optical spectroscopy data
Spectral-SpecPro helps with the manipulation of optical spectroscopy data. Spectral takes files produced by Jasco instruments (uv-vis absorbance, fluorescence, circular dichroism readings as a function of wavelength, temperature, or time) and facilitates basic operations such as unit conversion (CD spectra), conversion into the format taken by CDPro (estimation of secondary structure; CD spectra), scatter correction (absorbance spectra), smoothing, re-sampling of the x-axis, and generic... -
24
Pootle Django
Online translation tool
Pootle is written in Python using the Django framework and therefore can be installed on any web server that supports serving WSGI applications. Key localization file formats are supported, including Gettext PO, XLIFF, Java .properties, PHP arrays and many more supported by the Translate Toolkit. Ensures the best quality localizations by automatically detecting common errors made by translators. -
25
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).
