Scratchpad training

Vince Smith & Ed BakerNatural History Museum, London, UK

Training session

Virtual BiodiversityViBRANT

Overview of the day

• Expectations, introductions & goals• Overview presentation (30-40 minutes)

• Overview of http://scratchpads.eu (10 minutes)

• Training course options- Basic training (2-5 hours)

- Advanced training (3 hours)

- Publication tool (1 hour)

• Final Q&A• Feedback form

Why Scratchpads?

21st Century taxonomy

• Inventory the Earth’s species• Document their relationships• “Publish” & apply these data

Goal…

• 1.8 M described spp. (10M names)• 300M pages (over last 250 years)• 1.5-3B specimens

Data set…

People…• 4-6,000 scientists• 30-40,000 “pro-amateurs”• Many more citizen scientists?

The challenge for modern taxonomists

Towards a solutionThe European Distributed Institute of Taxonomy

• A Network of Excellence (NoE) • 29 leading European, North American, & Russian natural history collections-based institutions• Circa 12M €, funded under EU FP6• March 2006 - February 2011

Products…• Funding• Training & outreach• Websites• Integrated scientific activities• Inventories• Computer tools

Your data1

“Published” & reviewedon your site

3Uploaded &

tagged

Fast Intuitive Fit for use

What is a Scratchpad?A website for you & your community

ScratchpadsOverview

• Hosted websites for taxonomists• Research & publication platform • Modular (Drupal) & flexible • Supports the taxonomic workflow• Bottom-up design, agile dev.• Ecosystem of communities (200)• 2,500+ users (unpaid) from 2007

http://scratchpads.eu

ScratchpadsA multisite implementation of Drupal

Scratchpad Application FormFree to any individual or community

Flexible Template SiteWith easy navigation

Sites: 200+

Users: 2500+

Pages: 300k+

Circa 2 new sites/wk.

Since Mar. ‘07

10% access per mnth

An ecosystem of communities

40% accessed per mnth

Sustaining ScratchpadsViBRANT: Building on EDIT & the Scratchpads

“To set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research”

• A Virtual Research Environment (Scratchpads) where users can safely store, share and manage their research information.

• Analytical services for users to build identification keys and phylogenetic trees.

• A publication platform for users to automatically compile taxonomic manuscripts from their research database.

• A portal for users to centrally access publicly accessible biodiversity research information and literature.

• Training, support & sociological study, helping research communities to use these tools and services.

• A standards compliant technical architecture that can be sustained by the biodiversity research community.

ViBRANT logistics• Starts December 2010 (36 months)• Project website (http://vbrant.eu)• Virtual Research Communities, CP-CSA, EU FP7• €6.2M Euros (EU Contribution €4.75M)• 17 Partners in 9 countries, 603 person months

Collaboration…• ESFRI Projects: LifeWatch, ELIXIR & EMBRC• GBIF - controlled vocabularies, nodes & observational data recording• PESI, 4D4Life & related EU projects• Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library• South African National Biodiversity Institute & Atlas of living Australia

SERVICEWP5. Data

WP6. Publishing

WP4. StandardsWP8. Mobilisation

RESEARCHWP2. Architecture

WP7. Literature

NETWORKINGWP3. Training

ViBRANT Project planThe “chromosome”

ScratchpadTechnicalOverview

Scratchpad Object Model

http://scratchpads.eu/sites/scratchpads.eu/files/Scratchpad_Object_Model.pdf

Scratchpad managementScalable & sustainable technology

One virtual machine, open-source, self-archiving, backed-up, multi-site configuration(easy to move & upgrade, secure & reliable, screencasts, low admin., low marginal costs)

Hardware, software & user support

Scratchpad Developers Site

http://dev.scratchpads.eu/

Scratchpad SVN

http://svn.scratchpads.eu/viewvc

ScratchpadFunctionality

Summary

TaxonomyTaxonomy import, management and

navigation

Bibliographic data

Reference manager / Endnote support for bibliographies

Images

Image galleries,image upload & annotation

Phylogeny

Nexus / Newick import for visualizing phylogenies

Character Matricies

Molecular & morphological character matricies (discrete, morphometric and text characters)

Distribution Maps

Presence absence country maps

Specimens & locations

Specimen & location records (DwC)

Pages, Forums, Blogs, Newsletters

Web fora with e-mail integration

User blogs

Static web pages

Newsletters with e-mail integration

Mass Import

Import from CSV text file to any content type

Create & switch between content in any language

Multilingual Support

Administration

Simple & advanced admin.

AutoTag content(automatically adds structure)

Private Groups

Customized user profiles

Putting itall together

- an example site

Scratchpad structure

Taxonomybiblio

Content typesimage page

taxon page view

term 1

term 2

term 3

node view

list view

custom view

Knowledgebase on a family of flies

General Information

Special Information

User Comments

TaxonomyTaxonomy import, management and

navigation

Classification

‘Content’ menu

Image galleries

Link to image details

Image details

Classification and other tags

Virtual BiodiversityViBRANTSpecies page

Nomenclatureand taxonomy

Images

Bibliography

Specimen

Specimen map

Links Pages

Authors & Sources

Species description

Countries map

Glossary

Definition of term

Explanation

Character evolution

character matrix

export to SDD and Nexus

Milichia online revision

PhylogenyNexus / Newick import for visualizing phylogenies

Pages, Forums, Blogs, Newsletters

Web forums with e-mail integration

User blogs

Rich text editor

Newsletters with e-mail integration

Special functions

Multilingual support

Private groups – an area on your site that is visible only to selected users

Autotagging – automatically add structure to your content

Paper publication

User Support

Getting help

http://scratchpads.eu/help

The Sandbox

Built in help, the FAQ & issues queue

Screencasts, but…

Questions?

Scratchpad Training

http://training[X].taxon.name

Username: usernamePassword: password

Sites will be available for 2 weeks

Scratchpad Log-in

http://scratchpads.eu/scratchpad-training-filesScratchpad Training Files

http://carnidae.myspecies.info/Example Completed Site - Carnidae

Scratchpad training

Technology

DESCRIPTION OF A MACHINE ARCHITECTURE FOR …tack.sourceforge.net/olddocs/em.pdf · DESCRIPTION OF A MACHINE ARCHITECTURE FOR USE WITH ... (a cache or microprogram scratchpad memory)

Data Scratchpad Prefetching for Real-time Systems

Analyse des Einﬂusses der Zeitscheibenlange beim ...ls12- · PDF fileDiplomarbeit Analyse des Einﬂusses der Zeitscheibenlange beim¨ RoundRobin-Scheduling in Cache- und Scratchpad-basierten

Dynamic Binary Translation for Embedded Systems with Scratchpad Memory

FPGA implementation of a Cache Controller with … · FPGA implementation of a Cache Controller with Conﬁgurable Scratchpad ... around the MicroBlaze softcore ... Cache Controller

Working with ScratchPad RAMS for MIPS32® Cores Application Note · 2018. 8. 14. · 4 Working with ScratchPad RAMS for MIPS32® Cores Application Note, Revision 02.01 1 Introduction

A DYNAMIC CODE MAPPING TECHNIQUE FOR SCRATCHPAD MEMORIES ...aviral.lab.asu.edu/temp/publications/thesis/AmitThesis.pdf · A DYNAMIC CODE MAPPING TECHNIQUE FOR SCRATCHPAD ... A DYNAMIC

Exploiting Statistical Information for …sridevan/index_files/tvlsi-00168-2005.R1.pdfExploiting Statistical Information for Implementation of Instruction Scratchpad Memory in

CIS 199 Test 01 Review. Computer Hardware Central Processing Unit (CPU) Brains Operations performed here Main Memory (RAM) Scratchpad Work

Scratchpad Requirements Exercise

Improving Scratchpad Allocation with Demand-Driven …jingling/papers/cases10.pdf · Improving Scratchpad Allocation with Demand-Driven Data Tiling ... School of Computer Science

A summary of Scratchpad functionality

Memory Allocation via Graph Coloring using Scratchpad Memory Tomyo Maeshiro TomyoMaeshiro@my.unt.edu Software Engineering Language Lab UNT April 29,

Mathcad Prime 2 - Qucosa: · PDF filePDMLink reference management Requirements / Integrity Inside Creo as a scratchpad Published APIs Input controls Include Hyperlinks support Customizable

A Bibliography of Publications about the AXIOM (formerly ...ftp.math.utah.edu/pub/tex/bib/axiom.pdf · A Bibliography of Publications about the AXIOM (formerly, Scratchpad) Symbolic

One Pass Distinct Sampling - Oracle Scratchpad | Just ... procedures in dbms_stats package ... One pass distinct sampling----- contains same number of distinct values.

Scratchpad Memories: A Design Alternative for Cache On-chip Memory in Embedded Systems

ANALYZING THE BENEFITS OF SCRATCHPAD MEMORIES FOR

Dynamic Binary Translation for Embedded Systems with Scratchpad Memory José A. Baiocchi Paredes Department of Computer Science University of Pittsburgh

A Dynamic Code Mapping Technique for Scratchpad Memories in Embedded Systems