Bruno Vieira

Login: bmpvieira

Company: Queen Mary Uni. of London

Location: London

Bio: PhD Student at @wurmlab; @mozillascience Fellow; Founder of @bionode;

Blog: http://bmpvieira.com

Blog: http://bmpvieira.com

Member of

2. BioJS
3. biojupyter
4. bionode
5. Computational Biology & Population Genomics Group
6. LNUG
7. MozFellows organized events
8. Open Reproducible Biology
9. null
10. null
11. null

Repositories

2017-fellows-sf

2017 MozFellows Workweek - SF

adventure-time

a web based environment for doing nodeschool adventures

afra

Genome Annotation for the Masses

afra-environment

Dockerfile for Trusted Build of the image with the Afra project dependencies

allbio14

Talk for TGAC - AllBio 2014

all-contributors

? Recognize all contributors, not just the ones who push code ?

architect

Architect is a Jekyll theme for GitHub Pages

art-of-node

:snowflake: a short introduction to node.js

assembly14

MSc Bioinformatics - QA and Assembly

assembly-exercise

Shotgun sequencing of text, in CGI script form

assemblyline

Automatically exported from code.google.com/p/assemblyline

asset-rack

Static Web Framework for Nodejs

automarking

Auto correct and generate reports for exams results stored in Dat

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

aws-stream

Node.js Stream interface for Amazon Web Services (AWS)

bam.iobio.io

http://bam.iobio.io

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bignumber.js

A JavaScript library for arbitrary-precision decimal and non-decimal arithmetic

bioinformaticianad

Hiring a genomicist

bioinformatics

Tools for bioinformatics

bionode-dat-noflo-fetch

null

bionode-dat-noflo-nodejs

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bioseq-js

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

bmpvieira.github.io

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ccs14

Lightning talk (5 min) given at the Citizen Cyberscience Summit 2014

cgrsuffix.github.com

cgr for suffix trees

classdojo-matrix

ClassDojo Coding Challenge: Finding the Minimum Weight Path Through a Matrix

cobig2

AngularJS app that uses many APIs. Used in the new CoBiG² website.

cobig2_content

Content for the CoBiG² website (cobig2.com), written in markdown.

CodeMirror

In-browser code editor

concurrent-stream

null

contributor_covenant

Pledge your respect and appreciation for contributors of all kinds to your open source project.

coreos-vagrant

Minimal Vagrantfile for CoreOS

cpat

Automatically exported from code.google.com/p/cpat

cw14

Lightning talk (2 min) for the Collaborations Workshop 2014 at the Software Sustainability Institute

cw15

Bionode Demo at CW15

cy-rest-node

Node.js examples for cyREST module.

dalliance

Interactive web-based genome browser.

dat

real-time replication and versioning for large tabular data sets. pre-alpha!

dat-elife

Fetch elife XML from AWS S3 into Dat

datscript

A compile-to-JSON data pipeline scripting language

decker

Browserifiable Web Presentations

deck.js

Modern HTML Presentations

design

Stuff that I've made in inkscape, gimp, etc, for various purposes.

dgi-db

Rails frontend to The Genome Institute's drug gene interaction database.

dld

File downloader with partially-downloading support

docker-adventure-time

Base docker image for adventure-time workshops

docker-browser-server

Spawn and expose docker containers over http and websockets

Dockerfiles

My Dockerfiles. Trusted Builds also available in the Docker registry

docker-gc

garbage collect containers.

dotfiles

Some configs that I share among servers

expose-bash-over-websockets

expose bash over websockets

fellows-class-2016

The go-to place for materials, contributions and work for the 2016 Mozilla Fellows for Science.

Gadgetbridge

A free and cloudless replacement for your gadget vendors' closed source Android applications. Pebble and Mi Band supported.

GeeFuTu

Nothing to see here

GeeFuTu_JS_OLD

null

gene.iobio

demo website for gene search bar and gene visualization

genevalidatorapp

A web wrapper for GeneValidator

genomeinformatics.github.io

Homepage of the Genome Informatics Section

genomics-fetchers

Common back-end code for Browser-based genomics.

genomics-notebooks

IPython notebooks to teach Genomics and Population Genetics

GEODiver

null

get-dat

A command line tutorial to learn dat

git

Git Source Code Mirror - This is a publish-only repository and all pull requests are ignored. Please follow Documentation/SubmittingPatches procedure for any of your improvements.

gitbook

Command line utility for generating books and exercises using GitHub/Git and Markdown

gitter-irc-bot

:speech_balloon: Bot that synchronises messages from gitter and irc

GSoC

OBF Google Summer of Code

gulp-reveal

HTML to Reveal.js

HackDay-scribbles

misc code and scribbles from our hack days

heroku-dat-template

A simple Heroku app template for deploying Dat

hexbin

community curated list of hexagon logos

homebrew

:beer: The missing package manager for OS X.

host

Place to host files

http-browserify

node's http module, but for the browser

iobio

null

isuckattimezones

Quickly figure out time in other timezones.

jbrowse

AJAX Genome Browser

jmazz.me

null

js-bioinformatics-exercise

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js-local-vcf

Javascript local VCF and Tabix index file parsing and processing

khmer-protocols

null

KMC

Fast and frugal disk based k-mer counter

labjolly14a

Talk about the PSMC, given in the Evolution Group Lab Jolly at the Queen Mary, University of London.

levelgraph

Graph database JS style for Node.js and the Browser. Built upon LevelUp and LevelDB.

listen-to-wikipedia

Live, generative music from Wikipedia edits

meeting_notes

Notes from various scientific meetings and presentations I've attended

mentorship-program

14 week online mentorship program on Working Open starting March 2017

mjc

A python implementation of the Minimum Jump Cost dissimilarity algorithm.

mozfest16-lightning-talks

Lightning Talks from the Mozilla Festival October 28-30, 2016

mozfest2015-session

A starting point for building graphs with Cytoscape.js during the MozFest 2015 open science session

moz-fest-science-viz

Data Visualization Tutorial for Mozilla Science!!!

msl-gantt

[project] gantt chart for msl

msmc

Implementation of the multiple sequential markovian coalescent

msmc2

null

msmc-tools

Tools and Utilities for msmc and msmc2

nextflow-playground

Repo to test and play with Nextflow.io

ngs-analysis

Fork of https://code.google.com/p/ngs-analysis

nixpkgs

Nix Packages collection

nix-user-chroot

Run nix in a lightweight chroot container

node-browserify

browser-side require() the node.js way

nodeschool-dockerfiles

dockerfiles for nodeschool

nodeschool-interactive

interactive nodeschool online

noflo-bionode

null

noflo-nodejs

Node.js runtime environment for NoFlo UI

noflo-ui

NoFlo Development Environment

open-data-training

Development of an open data training program for Mozilla Science Labs.

open-retractions

:bangbang: :page_facing_up: :mag: an API and web interface to check if a paper has been retracted

open-source-templates

:octocat: Issue and Pull Request Template Generator featuring Chtulhu and Lewis Carroll

pace-stream

Stream interface for the Node.js module pace

parallel-transform

Transform stream for Node.js that allows you to run your transforms in parallel without changing the order

pgg48

Small talk given at the outreach event for the Population Genetics Group 2015 meeting

PKGBUILD

My Archlinux PKGBUILDs files

plotly.js

The open source javascript graphing library that powers plotly

PRoot

chroot, mount --bind, and binfmt_misc without privilege/setup

proot-static-build

Build static variants of PRoot

psmc

null

python101

Python 101 course slides

python101-administrative

Python 101 course administrative stuff

repro-case-studies

Reproducibility case study contributions

request

Simplified HTTP request client.

requesturl-stream

NPM module that wraps request to allow Stream of URLs as input

reveal.js

The HTML Presentation Framework

ruse.js

A lightweight WebGL library built for plotting large datasets.

s3policy

S3 Upload/Download Policy Generator for Node.js

sandbox

work place for new or broken containers

sanger14

null

sciencetoolbox

An index of open scientific software

scripts

Random scripts repo (for when using gist isn't the best).

Seeing-Theory

A visual introduction to probability and statistics.

seminar14

Talk given in a seminar at the Queen Mary, University of London.

sequenceserver

Intuitive local web frontend for the BLAST bioinformatics tool

shields

Shields badge specification, website and default API server

simple-corsproxy

Proxy to access resources that lack the Access-Control-Allow-Origin * header

skulpt

Skulpt is a Javascript implementation of the Python programming language

SlickGrid

A lightning fast JavaScript grid/spreadsheet

SOAPdenovo2

Next generation sequencing reads de novo assembler.

ssea

Automatically exported from code.google.com/p/ssea

SSMPG2017

Repository for the Data challenge about Software and Statistical Methods for Population Genetics (SSMPG 2017)

studyGroup

Gather together a group to skill-share, co-work, and create community

supercool-framework

null

switch

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

taxonomer.iobio

null

temp

null

testwatable

Simple node.js express with watable to display a simple sortable table

the-graph

SVG custom elements for FBP graph editing and visualization. Used in https://github.com/noflo/noflo-ui

threejsboilerplate

Boilerplate for three.js

tool-stream

Node.js module for working with Streams of objects.

TriFusion

Streamlining phylogenomic data gathering, processing and visualization

try-bionode

try dat using docker

understanding-npm

A regularly updating survey of the npm community

wiki

Federated Wiki - node server as npm package

WOW-2017

Mozilla Science Lab's Working Open Workshops in 2017

WOW-SA

Mozilla Science Lab's Working Open Workshop in Cape Town South Africa

wurmlab-meeting14a

Talk given at wurm lab meeting, before allbio14.

wurmlab-meeting15a

Bionode demo for a wurmlab meeting

xhr

A small xhr wrapper

xml2json-stream

Converts XML to JSON, using Streams and sax. This can be used with above-memory-limits XML files, as long as they're mostly composed of a repetitive tag.

you-probably-dont-want-an-object

talk given at LondonJSConf, 2014

Commits To