Explore @elifesciences Open Source projects

eLife Sciences Publications Ltd (@elifesciences)

elifesciences

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lens

A novel way of seeing content

sciencebeam-parser

A set of tools to allow PDF to XML conversion, utilising Apache Beam and other tools. The aim of this project is to bring multiple tools together to generate a full XML document.

elife-xpub

eLife is an open-access journal and technology provider that publishes promising research in the life and biomedical sciences. This is their implementation of a submission and peer review system based on Coko PubSweet and xPub.

datacapsule-crossref

Retrieve and extract citations from Crossref data

Jupyter Notebook

sciencebeam-gym

ScienceBeam Gym

elife-article-xml

Full XML of all eLife articles including each revision.

elife-bot

tools for creating an automatic publishing workflow.

journal

eLife is an open-access journal that publishes promising research in the life and biomedical sciences

elife-tools

Tools for using article data in Python

elife-continuum-documentation

ppp project related files and prototypes

lens-browser

Lens Article Browser

lens-converter

A client-side NLM to Lens converter. Based on Substance.Converter.

elife-articles

xml of elife articles

refract

Convert NLM XML files into the Lens JSON

builder

elife-jenkins-workflow-libs

Common steps used in eLife's Jenkins Pipelines

citation-context

Jupyter Notebook

lens-indexer

Lens Indexer based on ElasticSearch.

rds-example

Stand-alone example of a reproducible document stack article

api-raml

RAML for the eLife Sciences API

pattern-library

Pattern library driving https://elifesciences.org, the eLife journal.

reference-schematron

sciencebeam-trainer-delft

Wrapper around https://github.com/kermitt2/delft

proofreader-php

proofreader-php is a tool for enforcing opinionated coding standards and conventions through static analysis of the code.

sciencebeam-airflow

Airflow pipeline for ScienceBeam related training and evaluation

jats-scraper

standalone article xml scraper for the pppp project

elife-crossref-xml-generation

Crossref deposit of journal articles

lax

lens-reader

The Lens Reader as a module, for custom app integration

basex-validator-docker

XML Validation service built on BaseX for validating XML against elife's schematron files

lens-elife

eLife integrations of Lens with custom extensions as well as official bundle

publisher-xml-fragment-examples

isolated-drupal-behat-extension

Extension for Behat that tests Drupal sites in isolation.

lens-outline

Visually outlines Substance documents.

search

journal-cms

jats-generator

JATS XML generator

jats-xml-to-pdf

peerscout

PeerScout® is a web application and machine learning trained API for suggesting peer reviewers from an existing pool, based on attributes of the papers they have reviewed and written

bot-lax-adaptor

XML-mapping

Mapping the XML to new Continuum requirements and build of a new Kitchen sink

eLife-JATS-schematron

Schematron for all JATS eLife content

elife-pdfs

pdf versions of elife articles

threadbare

A partial replacement for eLife's usage of Fabric 1.x and Paramiko.

cermine-docker

data-science-peertax

Data Science project looking into the Peer Review Taxonomy

Jupyter Notebook

elife-flux-cluster

Definition of eLife's k8s cluster and deployments to it. Automatically applied via Flux.

medium

eLife Medium articles API

api-dummy

Dummy implementation of the eLife Sciences API

lens-sandbox

Lens Development Environment

elife-article-scheduler

manage scheduling future publications for eLife Continuum

bus-sdk-php

PHP SDK for the eLife Sciences bus [in development]

elife-metrics

schematron-wiki

This contains the markdown from gitbook for schematron.

lens-starter

Minimal Lens integration, use as a starting point for development

elife-api

data-hub-ejp-xml-pipeline

Data pipeline for loading eJP Xml files from S3 bucket into Bigquery

data-science-dags

sciencebeam-utils

ScienceBeam Utils

peerscout-dags

citation-sentiment-analysis

Jupyter Notebook

elife-data-hub-utils

Utility functions related to elife-data-hub

data-hub-airflow-image

create custom airflow image used for running data-hub pipeline

enhanced-preprints-client

Enhanced Preprints client application

data-hub-core-airflow-dags

builder-configuration

Contains non-sensitive Salt formulas configuration

patterns-php

PHP implementation of the eLife patterns

data-pipeline-sql-prototype

A central place for resources relating to the eLife Data Pipeline tools

bigquery-views-manager

BigQuery Views Manager

packer-test

files for testing packer

elife-drupal-cookbook

elife version of drupal cookbook

populate-elife-api

scripts for getting elife xml, parsing them, and populating our REST api

developer-resources

Are you a developer or hacker interested in using eLife's open-source resources? This page is for you! If you do build something using our code, we'd love to hear at [email protected] (we may be able to help you grow your project).

elife-alfred-formula

JATs-xml

eLife upgrade to JATS xml

api-gateway-formula

elife-dashboard

publishing dashboard for eLife Continuum

enhanced-preprints-import

Enhanced Preprints import system

elife-kickstart

Build script to make it easier to start building a distribution for a new Drupal project.

sciencebeam-editor

eif-article-json

elife-data-hub-charts

api-client-php

PHP client for the eLife Sciences API

journal-cms-formula

citerank

Calculates PageRank over citation data

builder-base-formula

lens-library

Library of eLife Articles, used as a landing page at lens.elifesciences.org

elife-metrics-formula

elife-flux-test

Declares the deploys to kubernetes-aws--flux-test cluster using fluxcd

lens-s3

elife-article-xml-continuumtest

Testing repository. Contents may be DELETED at any time.

data-hub-api

elife-utility-scripts

a collection of utility scripts used at eLife

api-sdk-php

PHP SDK for the eLife Sciences API

elife-crossref-feed

code to support uploading info to crossref on PAW articles

pubpub-css

To enable version control of the CSS in PubPub's static page system

elife-website

sciencebeam-trainer-grobid

ScienceBeam Trainer for GROBID

hypothesis-dummy

Minimal dummy to stand in for Hypothes.is inside eLife's testing infrastructure

bioprotocol-service