Open Source Python Scientific/Engineering Software

Grafana OSS is a leading open-source visualization and observability platform that lets you query, visualize, alert on, and explore your data—regardless of where it’s stored. With support for 100+ data source plugins (such as Prometheus, Loki, Elasticsearch, InfluxDB, SQL/NoSQL databases, OTel, and more), you can unify metrics, logs, traces, and other observability signals in one place. Grafana OSS empowers you to build dynamic, reusable dashboards with rich visualizations, template variables, interactive filtering, and cross-panel linking. Its Explore mode enables ad-hoc queries and side-by-side comparisons of time ranges, queries, and data sources. Grafana also includes built-in alerting, allowing you to define threshold-based rules and send notifications to external systems (e.g. Slack, PagerDuty, OpsGenie). Backed by a strong community (https://grafana.com/community/) and open governance, Grafana OSS is free to use, modify, and deploy under the AGPL-3.0 license.

The goal of PyTables is to enable the end user to efficiently and easily manipulate large datasets (both homogenous, i.e. arrays, and heterogenous, i.e. tables) on a persistent, hierarchical way.

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

The Flamenco search and browse interface framework uses hierarchical faceted metadata to allow users to both refine and expand queries, while maintaining a consistent representation of a collection and seamlessly integrating keyword queries.

ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories. The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics, morphology, dominance, and spatial location of each specimen collected in the field.

This is a prototype implementation of "A Network of Ideas" (ANOI) content system.

AGTK is a suite of software components for building tools for annotating linguistic signals, time-series data which documents any kind of linguistic behavior (e.g. audio, video). The internal data structures are based on annotation graphs.

This is a testbed for projects of personal interests, especially academic projects.

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

New version moved to http://github.com/ctuning/ck Collective Mind framework (cM) is an open-source plugin-based schema-free repository and infrastructure for collaborative, systematic and reproducible research and experimentation. This 3rd version (started in 2006) helps to implement, preserve, share and reproduce the whole experimental setup as connected modules and data. cM uses crowdsourcing to leverage knowledge and computational resources of multiple users. For example, it includes multi-objective GCC, LLVM and ICC auto-tuning scenarios using shared benchmarks, codelets, data sets, tools, and combined with classification and predictive models. cM includes OpenME interactive interface to open up and expose internals of various third-party tools such as GCC, LLVM, run-time systems, etc. and connect them to cM through dynamic plugins that allows online analysis and tuning of programs and architectures. Live repo: http://c-mind.org/repo

ConDEnSE (Confidential Data Enabled Statistical Exploration) will be a web-based environment for statistical analysis of confidential data from various database sources, based on Plone and R, and using the Jackknife method of confidentiality protection.

Crow - Computational Representation Of Whatever. A platform for the integration and mining of complex and distributed data. Represents cross-linked semantic web documents as a network of software objects and offers easy ways to filter, and sort them.

DesktopTools is a collection of small utillities which help to make your daily life easier. Since the tools themself are rather small (projectwise) I keep them not as individual projects, but have them under this collective name.

A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.

FastVersion is a Qgis plugin for data versioning in a Postgis database. This plugin provides data versioning to tables with geometry stored in postgis. It allows to create, changes and eliminate versions, and within each version , to insert, modify and eliminate elements. It is possible carry out the processes of “post” from one version to another, with conflict resolution functionality. The system uses algorithms and data structures so that information is not duplicated each time a version is created. We recommend downloading it from the Qgis app. Plugins->Manage and Install Plugins->Settings->Show also experimental plugins Plugins->Manage and Install Plugins->Search FastVersion If downloaded from sourceforge, it must be unzipped in \.qgis2\python\plugins

A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org). Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.

<This project has been completely rewrote and transformed into a new one: https://sourceforge.net/projects/deday/. 2013/06/26> The graphic user interface for DEDA (DEmography Data Analysis), a scientific software package fitting survivalship data to a number of distributions using maximum likelihood (ML) method. Currently, Weibull (2p), Gompertz and Gompertz-Makeham are supported. IMPORTANT NOTICE: Only the GUI is provided here. In order to perform the analysis, one also need the DEDA computation core program. Please email a request to me, entitled: 'Request for DEDA computation core', if you wish to have a copy.

In Green Cloud here is a central global server which does the work of global database management along with providing complex analysis services for the users (farmers, scientists) through the client machines and the public access web portal. The existing agricultural databases throughout the world can also be used for inference purposes and their data may also be updated by our server. The meteorological servers can be accessed for climate data.This server-client architecture mandatory in present and even near-future circumstances as the client machine has to be low-power and low-cost for the feasibility of the system in Indian context. Therefore, the complex analysis (Expert system analysis in accordance with world-wide data) has to be done on server. The environment data is collected via sensors is uploaded to the website

KML is a knowledge base with support of logical modeling. Advanced model is used to represent knowledge as a set of statements similar to natural language sentences. This project hosts a set of model storage library and server (vrb-ols) and clients.

Kura is a complete, professional system for the handling of linguistic data, especially fieldwork data from small-corpus languages. It allows users to enter texts in any language and analyze those texts

A Python/Gtk application to manage groups of users stored in an LDAP database, using data from X509 certificates imported from files or LDAP servers maintained by certificate authorities. These groups are used to create grid-map files used by the Globus

LightProfiler – application for performance analysis of the Oracle databases. It generates detailed resource profile for extended SQL trace files (10046 event), containing information about consuming of response time (by events, by cursors, etc.), data files usage, error analysis (SQL, PL/SQL) and much more. Also it contain tools for additional processing of trace files (extract session data, splitting files) and for management of database's sessions (disconnecting, tracing, monitor parameters, blocking locks, events and etc.)

NTuple is a Python module used by high-energy physicists and astrophysicists to easily and efficiently access ntuple data stored in large ROOT data stores. Specifically, NTuple provides a friendly Pythonic interface to TNtuples and TTrees stored in TFiles

The NetEpi project is developing open-source, network-enabled tools for epidemiology and public health practice.