From ce2ebd5db3b8ae04b234e499c6f4e2ec37bd1f97 Mon Sep 17 00:00:00 2001 From: Maneesha Sane Date: Fri, 3 May 2024 19:55:48 -0400 Subject: [PATCH] rm projects from includes --- _includes/projects/active-papers.html | 12 ------------ _includes/projects/archer.html | 11 ----------- _includes/projects/astropy.html | 10 ---------- _includes/projects/biostars.html | 14 -------------- _includes/projects/cyclus.html | 16 ---------------- _includes/projects/ecodata-retriever.html | 9 --------- _includes/projects/eff-phys.html | 14 -------------- _includes/projects/gap.html | 12 ------------ _includes/projects/genomics-virtual-lab.html | 11 ----------- _includes/projects/git-rdm.html | 11 ----------- _includes/projects/ipfs.html | 14 -------------- _includes/projects/iplant.html | 13 ------------- _includes/projects/jors.html | 10 ---------- _includes/projects/khmer.html | 12 ------------ _includes/projects/macroeco.html | 15 --------------- _includes/projects/magetbrain.html | 13 ------------- _includes/projects/mahotas.html | 9 --------- .../projects/math-education-resources.html | 14 -------------- _includes/projects/mothur.html | 13 ------------- _includes/projects/msl.html | 18 ------------------ _includes/projects/nipy.html | 11 ----------- _includes/projects/open-tree-of-life.html | 15 --------------- _includes/projects/pecan.html | 13 ------------- .../practical-computing-for-biologists.html | 14 -------------- _includes/projects/pymc.html | 12 ------------ _includes/projects/pyne.html | 15 --------------- _includes/projects/pyrdm.html | 14 -------------- _includes/projects/ropensci.html | 11 ----------- _includes/projects/scikit-bio.html | 17 ----------------- _includes/projects/scikit-image.html | 10 ---------- _includes/projects/sharelatex.html | 14 -------------- _includes/projects/stat-545.html | 10 ---------- _includes/projects/tec.html | 10 ---------- 33 files changed, 417 deletions(-) delete mode 100644 _includes/projects/active-papers.html delete mode 100644 _includes/projects/archer.html delete mode 100644 _includes/projects/astropy.html delete mode 100644 _includes/projects/biostars.html delete mode 100644 _includes/projects/cyclus.html delete mode 100644 _includes/projects/ecodata-retriever.html delete mode 100644 _includes/projects/eff-phys.html delete mode 100644 _includes/projects/gap.html delete mode 100644 _includes/projects/genomics-virtual-lab.html delete mode 100644 _includes/projects/git-rdm.html delete mode 100644 _includes/projects/ipfs.html delete mode 100644 _includes/projects/iplant.html delete mode 100644 _includes/projects/jors.html delete mode 100644 _includes/projects/khmer.html delete mode 100644 _includes/projects/macroeco.html delete mode 100644 _includes/projects/magetbrain.html delete mode 100644 _includes/projects/mahotas.html delete mode 100644 _includes/projects/math-education-resources.html delete mode 100644 _includes/projects/mothur.html delete mode 100644 _includes/projects/msl.html delete mode 100644 _includes/projects/nipy.html delete mode 100644 _includes/projects/open-tree-of-life.html delete mode 100644 _includes/projects/pecan.html delete mode 100644 _includes/projects/practical-computing-for-biologists.html delete mode 100644 _includes/projects/pymc.html delete mode 100644 _includes/projects/pyne.html delete mode 100644 _includes/projects/pyrdm.html delete mode 100644 _includes/projects/ropensci.html delete mode 100644 _includes/projects/scikit-bio.html delete mode 100644 _includes/projects/scikit-image.html delete mode 100644 _includes/projects/sharelatex.html delete mode 100644 _includes/projects/stat-545.html delete mode 100644 _includes/projects/tec.html diff --git a/_includes/projects/active-papers.html b/_includes/projects/active-papers.html deleted file mode 100644 index 4a012eb68..000000000 --- a/_includes/projects/active-papers.html +++ /dev/null @@ -1,12 +0,0 @@ -

- ActivePapers - ActivePapers - aims to make computational science more open and more reliable by - making computations reproducible and publishable. It is a file - format for storing computations, consisting of both code and data, - and it is also a software infrastructure for working with this - file format. -
- Contact: - Konrad Hinsen -

diff --git a/_includes/projects/archer.html b/_includes/projects/archer.html deleted file mode 100644 index 5cb3c5768..000000000 --- a/_includes/projects/archer.html +++ /dev/null @@ -1,11 +0,0 @@ -

- ARCHER - ARCHER - is the UK National Supercomputing Service, providing a world-class - supercomputer and invaluable computational resources, consultancy - and training for researchers who study problems with a global - impact. -
- Contact: - Mike Jackson -

diff --git a/_includes/projects/astropy.html b/_includes/projects/astropy.html deleted file mode 100644 index fd0ebc113..000000000 --- a/_includes/projects/astropy.html +++ /dev/null @@ -1,10 +0,0 @@ -

- Astropy - Astropy - is a community-driven package intended to contain much of the core - functionality and some common tools needed for performing - astronomy and astrophysics with Python. -
- Contact: - Erik Bray -

diff --git a/_includes/projects/biostars.html b/_includes/projects/biostars.html deleted file mode 100644 index 1cbe7670f..000000000 --- a/_includes/projects/biostars.html +++ /dev/null @@ -1,14 +0,0 @@ -

- Biostars - Biostars - is a bioinformatics, computational genomics and biological data - analysis question and answer forum. It is most used by biological - computational scientists and it addresses all levels of questions - regarding biological and computational data analysis. Biostars was - started by Istvan Albert in 2010 and has since grown to more than - 16,000 contributors with more than 120,000 posts on bioinformatics - and genomics. -
- Contact: - Josh Herr -

diff --git a/_includes/projects/cyclus.html b/_includes/projects/cyclus.html deleted file mode 100644 index 0041909a2..000000000 --- a/_includes/projects/cyclus.html +++ /dev/null @@ -1,16 +0,0 @@ -

- Cyclus - Cyclus, - the Next Generation Nuclear Fuel Cycle Simulator, is the - next-generation agent-based nuclear fuel cycle simulator, - providing flexibility to users and developers through a dynamic - resource exchange solver and plug-in, user-developed agent - framework. The goal of Cyclus is to enable a broad spectrum of - fuel cycle simulation while providing a low barrier to entry for - new users and agent developers. -
- Contact: - Katy Huff, - Paul Wilson, - Anthony Scopatz -

diff --git a/_includes/projects/ecodata-retriever.html b/_includes/projects/ecodata-retriever.html deleted file mode 100644 index 4bb6945a6..000000000 --- a/_includes/projects/ecodata-retriever.html +++ /dev/null @@ -1,9 +0,0 @@ -

- EcoDataRetriever - The EcoData Retriever - automates finding, downloading and cleaning up ecological datasets. -
- Contact: - Ethan White, - Ben Morris -

diff --git a/_includes/projects/eff-phys.html b/_includes/projects/eff-phys.html deleted file mode 100644 index e0fa111d0..000000000 --- a/_includes/projects/eff-phys.html +++ /dev/null @@ -1,14 +0,0 @@ -

- Effective Computation in Physics - Effective Computation in - Physics is a manual of programming and software skills aimed at - researchers in the physical sciences and engineering. This field guide to - effective scientific computing in Python covers: programming in Python, - important Python packages such as NumPy and Pandas, interaction with the - command line, software testing, version control, build systems, - documentation, publishing using LaTeX, how to manage collaborative - software development with GitHub, and even how to license your software. -
- Contact: - Katy Huff, Anthony Scopatz -

diff --git a/_includes/projects/gap.html b/_includes/projects/gap.html deleted file mode 100644 index fcda341d1..000000000 --- a/_includes/projects/gap.html +++ /dev/null @@ -1,12 +0,0 @@ -

- GAP - GAP is a free, open and - extensible system for discrete computational algebra, with - particular emphasis on Computational Group Theory. GAP provides a - programming language, a library of thousands of functions - implementing algebraic algorithms written in the GAP language as - well as large data libraries of algebraic objects. -
- Contact: - Alexander Konovalov -

diff --git a/_includes/projects/genomics-virtual-lab.html b/_includes/projects/genomics-virtual-lab.html deleted file mode 100644 index d99491126..000000000 --- a/_includes/projects/genomics-virtual-lab.html +++ /dev/null @@ -1,11 +0,0 @@ -

- Genomics Virtual Lab - The Genomics Virtual Lab - provides analysis tutorials and protocols, and scalable research - platforms on the cloud with easy access to reference data and - tools on demand. Tools include Galaxy, IPython Notebook, RStudio, - and environment modules for command-line users. -
- Contact: - Clare Sloggett -

diff --git a/_includes/projects/git-rdm.html b/_includes/projects/git-rdm.html deleted file mode 100644 index 9631fae41..000000000 --- a/_includes/projects/git-rdm.html +++ /dev/null @@ -1,11 +0,0 @@ -

- Git-RDM - Git-RDM - is a Research Data Management (RDM) plugin for the Git version control - system. It interfaces Git with data hosting services to manage the - curation of version controlled files using persistent, citable - repositories. -
- Contact: - Christian Jacobs -

diff --git a/_includes/projects/ipfs.html b/_includes/projects/ipfs.html deleted file mode 100644 index 2e6852505..000000000 --- a/_includes/projects/ipfs.html +++ /dev/null @@ -1,14 +0,0 @@ -

- IPFS - IPFS - is a system for managing generic content-addressable data in - a generalized - Markle graph and mutable references to that data over a - distributed, peer-to-peer network. For example, you could use the - same system to manage both your source code and your huge binary - datasets, transferring changes efficiently between any set of - nodes, and archiving past versions for as long as you like. -
- Contact: - W. Trevor King -

diff --git a/_includes/projects/iplant.html b/_includes/projects/iplant.html deleted file mode 100644 index a65853409..000000000 --- a/_includes/projects/iplant.html +++ /dev/null @@ -1,13 +0,0 @@ -

- iPlant Collaborative - The iPlant Collaborative - is cyberinfrastructure for scientists, educators, and students - working in all domains of life sciences. iPlant resources allow - users to analyze, manage, and store data and experiments, access - high-performance computing, and share results with colleagues. - iPlant is open source and funded by the National Science - Foundation. -
- Contact: - Jason Williams -

diff --git a/_includes/projects/jors.html b/_includes/projects/jors.html deleted file mode 100644 index 10ca93336..000000000 --- a/_includes/projects/jors.html +++ /dev/null @@ -1,10 +0,0 @@ -

- Journal of Open Research Software - The Journal of Open Research Software is an Open - Access journal featuring peer reviewed software metapapers - describing research software with high reuse potential and - full-length papers that cover different aspects of - creating, maintaining and evaluating open source research - software.
Contact: - Neil Chue Hong -

diff --git a/_includes/projects/khmer.html b/_includes/projects/khmer.html deleted file mode 100644 index 3856b2dc0..000000000 --- a/_includes/projects/khmer.html +++ /dev/null @@ -1,12 +0,0 @@ -

- khmer project - The khmer project - provides scripts and a library for analyzing, - filtering, and correcting DNA sequencing data. The project - implements efficient probabilistic data structures and lossy - compression algorithms for working with very large DNA sequencing - data sets. -
- Contact: - Titus Brown -

diff --git a/_includes/projects/macroeco.html b/_includes/projects/macroeco.html deleted file mode 100644 index 966870830..000000000 --- a/_includes/projects/macroeco.html +++ /dev/null @@ -1,15 +0,0 @@ -

- Macroeco - Macroeco - provides a comprehensive set of functions for analyzing empirical - patterns in ecological data, predicting patterns using theory and - models, and comparing empirical patterns to theory. Many major - macroecological patterns can be analyzed using this package, - including the species abundance distribution, the species and - endemics area relationships, several measures of beta diversity, - and many others. -
- Contact: - Mark Wilber, - Justin Kitzes -

diff --git a/_includes/projects/magetbrain.html b/_includes/projects/magetbrain.html deleted file mode 100644 index ba0e53d1d..000000000 --- a/_includes/projects/magetbrain.html +++ /dev/null @@ -1,13 +0,0 @@ -

- MAGeTBrain - MAGeTBrain - Given a set of anatomically labelled MR images (atlases) and - unlabeled images (subjects), MAGeT (Multiple Automatically - Generated Templates Brain Segmentation) produces a segmentation - (automatic labeling) for each subject using a multi-atlas voting - procedure based on a template library made up of images from the - subject set. -
- Contact: - Gabriel A. Devenyi -

diff --git a/_includes/projects/mahotas.html b/_includes/projects/mahotas.html deleted file mode 100644 index 22c95ca7c..000000000 --- a/_includes/projects/mahotas.html +++ /dev/null @@ -1,9 +0,0 @@ -

- Mahotas - Mahotas - is a computer vision and image processing library for Python based - on NumPy. -
- Contact: - Luis Pedro Coelho -

diff --git a/_includes/projects/math-education-resources.html b/_includes/projects/math-education-resources.html deleted file mode 100644 index bd7fa4b8b..000000000 --- a/_includes/projects/math-education-resources.html +++ /dev/null @@ -1,14 +0,0 @@ -

- Math Education Resources - The Math Education Resources - is a volunteer-run project that provides substantial learning - resources to undergraduate students taking math courses at UBC or - elsewhere. Our wiki provides free hints and peer-reviewed - solutions to previous final exam questions from UBC's math - courses. Students can search questions by topic, watch mini video - lectures for each topic, or use the difficulty ratings from their - peers to guide their studies. -
- Contact: - Bernhard Konrad -

diff --git a/_includes/projects/mothur.html b/_includes/projects/mothur.html deleted file mode 100644 index b311e6146..000000000 --- a/_includes/projects/mothur.html +++ /dev/null @@ -1,13 +0,0 @@ -

- mothur project - mothur is an open source and - portable software package that meets the bioinformatics needs of - the microbial ecology research community. It is particularly - useful for analyzing 16S rRNA gene sequences that have been - generated using a variety of sequencing platforms. We emphasize - making the software as easy to use as possible through our efforts - in maintaining a wiki, blog, and user forum. -
- Contact: - Pat Schloss -

diff --git a/_includes/projects/msl.html b/_includes/projects/msl.html deleted file mode 100644 index c54ff0953..000000000 --- a/_includes/projects/msl.html +++ /dev/null @@ -1,18 +0,0 @@ -

- Mozilla Science Lab - The Mozilla - Science Lab is helping a global network of researchers, tool - developers, librarians and publishers collaborate to further - science on the web, via collaboration, prototyping and educational - projects. Check - out projects they're - working on with the open science community, and join the - dicsussion on their - forum or their - community calls. -
- Contact: - Abby Cabunoc, - Arliss Collins, - Bill Mills -

diff --git a/_includes/projects/nipy.html b/_includes/projects/nipy.html deleted file mode 100644 index 5e08e9bb3..000000000 --- a/_includes/projects/nipy.html +++ /dev/null @@ -1,11 +0,0 @@ -

- NIPY - NIPY (Neuroimaging in - Python) is making it easier to do better brain imaging research, by designing - and implementing free and open-source algorithms and pipelines for the - analysis of data from neuroimaging experiments, and teaching neuroscientists - how to use them. -
- Contact: - Ariel Rokem -

diff --git a/_includes/projects/open-tree-of-life.html b/_includes/projects/open-tree-of-life.html deleted file mode 100644 index eeb6e48aa..000000000 --- a/_includes/projects/open-tree-of-life.html +++ /dev/null @@ -1,15 +0,0 @@ -

- Open Tree of Life - The Open Tree of Life - is building a comprehensive tree of all life. By enabling - community contribution of phylogenies (estimates of species or - other group relationships), and combining these phylogenies into a - single tree-of-life we capturing the depth of knowledge about - biodiversity on Earth, encouraging community comment and - refinement and preserving phylogenetic data in a readily reusable - way. -
- Contact: - Emily Jane McTavish, - Karen Cranston -

diff --git a/_includes/projects/pecan.html b/_includes/projects/pecan.html deleted file mode 100644 index 8ff694c02..000000000 --- a/_includes/projects/pecan.html +++ /dev/null @@ -1,13 +0,0 @@ -

- PEcAn Project - The Predictive Ecosystem Analyzer (PEcAn) - is an integrated ecological bioinformatics toolbox that provides tools to synthesize - plant and ecosystem data with mechanistic understanding encoded in ecosystem models. - PEcAn is not a model itself, but a platform for model parameterization and calibration - that wraps simulation models within a Bayesian framework. The PEcAn Project is an open - community of scientists, programmers, and educators and we welcome new contributions - and applications. -
- Contact: - David LeBauer -

diff --git a/_includes/projects/practical-computing-for-biologists.html b/_includes/projects/practical-computing-for-biologists.html deleted file mode 100644 index e086a9a94..000000000 --- a/_includes/projects/practical-computing-for-biologists.html +++ /dev/null @@ -1,14 +0,0 @@ -

- Practical Computing for Biologists - Practical Computing for Biologists - aims to teach scientists of all types essential computational - skills for data analysis. It assumes no pre-requisites other than - motivation, features the most useful tools that can benefit - researchers almost immediately, and explains how to use these - tools together. With a background level of comfort, researchers - can then go on to reap even more benefit from Software Carpentry - and other educational sites and courses. -
- Contact: - Steve Haddock -

diff --git a/_includes/projects/pymc.html b/_includes/projects/pymc.html deleted file mode 100644 index 4edcc371c..000000000 --- a/_includes/projects/pymc.html +++ /dev/null @@ -1,12 +0,0 @@ -

- PyMC - PyMC - is a Python module that implements Bayesian statistical models and fitting algorithms, - including Markov chain Monte Carlo. - Its flexibility and extensibility make it applicable to a large suite of problems. - Along with core sampling functionality, - PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics. -
- Contact: - Chris Fonnesbeck -

diff --git a/_includes/projects/pyne.html b/_includes/projects/pyne.html deleted file mode 100644 index f57000dc0..000000000 --- a/_includes/projects/pyne.html +++ /dev/null @@ -1,15 +0,0 @@ -

- PyNE project - PyNE, - the Nuclear Engineering Toolkit, is a suite of tools to aid in - computational nuclear science and engineering. PyNE seeks to provide - native implementations of common nuclear algorithms, as well as - Python bindings and I/O support for other industry standard - nuclear codes. -
- Contact: - Katy Huff, - Rachel Slaybaugh, - Paul Wilson, - Anthony Scopatz -

diff --git a/_includes/projects/pyrdm.html b/_includes/projects/pyrdm.html deleted file mode 100644 index a6755ba32..000000000 --- a/_includes/projects/pyrdm.html +++ /dev/null @@ -1,14 +0,0 @@ -

- PyRDM - PyRDM - is a Python-based library for research data management (RDM). - It facilitates the automated management and publication of software - source code and data via online, citable repositories hosted by - Figshare, Zenodo, or a DSpace-based service. The library - is open-source - and can be readily incorporated into scientific workflows to allow - research outputs to be curated and shared in a straight-forward manner. -
- Contact: - Christian Jacobs -

diff --git a/_includes/projects/ropensci.html b/_includes/projects/ropensci.html deleted file mode 100644 index fa7bdbf97..000000000 --- a/_includes/projects/ropensci.html +++ /dev/null @@ -1,11 +0,0 @@ -

- rOpenSci project - rOpenSci - is a software collective that provides R based tools to enable - access to scientific data repositories, full-text of articles, and - science metrics and also facilitate a culture shift in the - scientific community towards reproducible research practices. -
- Contact: - Karthik Ram -

diff --git a/_includes/projects/scikit-bio.html b/_includes/projects/scikit-bio.html deleted file mode 100644 index 70db50093..000000000 --- a/_includes/projects/scikit-bio.html +++ /dev/null @@ -1,17 +0,0 @@ -

- scikit-bio - scikit-bio - is a Python bioinformatics library based on the standard Python - scientific computing stack that implements core bioinformatics - data structures, algorithms, parsers, and formatters. scikit-bio - is the first bioinformatics-centric scikit, and arises from over - ten years of development efforts on PyCogent and QIIME, It is - intended to be useful both for students, who can use it in - conjunction with the accompanying interactive - textbook, - An Introduction to Applied Bioinformatics, - and for real-world bioinformatics developers. -
- Contact: - Greg Caporaso -

diff --git a/_includes/projects/scikit-image.html b/_includes/projects/scikit-image.html deleted file mode 100644 index bb763360b..000000000 --- a/_includes/projects/scikit-image.html +++ /dev/null @@ -1,10 +0,0 @@ -

- scikit-image - scikit-image - is a collection of algorithms for image processing. It is available free of - charge and free of restriction. We pride ourselves on high-quality, - peer-reviewed code, written by an active community of volunteers. -
- Contact: - Juan Nunez-Iglesias -

diff --git a/_includes/projects/sharelatex.html b/_includes/projects/sharelatex.html deleted file mode 100644 index 3854dcb82..000000000 --- a/_includes/projects/sharelatex.html +++ /dev/null @@ -1,14 +0,0 @@ -

- ARCHER - ShareLaTeX - is an online collaborative LaTeX editor designed to make LaTeX - more accessible to newcomers, and to make collaboration easier - between co-authors. Everyone can access the latest version, see a - full change history, and work with the same compatible LaTeX - environment. ShareLaTeX is available - hosted, - and is open source. -
- Contact: - James Allen -

diff --git a/_includes/projects/stat-545.html b/_includes/projects/stat-545.html deleted file mode 100644 index 6f660d72f..000000000 --- a/_includes/projects/stat-545.html +++ /dev/null @@ -1,10 +0,0 @@ -

- STAT 545 project - STAT 545 - at the University of British Columbia teaches students how to - explore, groom, visualize, and analyze data, and how to make all - of that reproducible, reusable, and shareable using R. -
- Contact: - Jenny Bryan -

diff --git a/_includes/projects/tec.html b/_includes/projects/tec.html deleted file mode 100644 index 270a2dd01..000000000 --- a/_includes/projects/tec.html +++ /dev/null @@ -1,10 +0,0 @@ -

- tec project - tec - provides utilities for a uniform and extensible API for easily - simulating vacuum thermionic energy conversion (TEC) devices. A few - models are supplied with the tec package, but others can be easily - added. -
- Contact: Joshua Ryan Smith -