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									                                           Archer E-Research Group

                                                      Project Agreement
                                                                                     To


       Queensland Facility for Advanced Bioinformatics
                                                                                     for

OVERVIEW of PROJECT TO PROVIDE COLLABORATION PORTAL SOFTWARE APPLICATIONS, SOFTWARE
                      TOOLS AS WELL AS IMPLEMENTATION, RESEARCH AND SUPPORT SERVICES

                                                                            Version 1.0

                                                                    Date: 3rd April 2008
Document Management

Release Information
Version           Date                  Name                                            Remarks

Version 8         7th March 2008        Andrew Alexander                                Ver 8


Distribution List
Name                     Organisation                    Versions               Title

Dominique Gorse          JCU                             V2.1, 3, 5,7,8         Manager QFAB

Frank Eilert             JCU                             V1.1, 3, 4, 5,6,7,8    Project Manager Archer

Andrew Alexander         Comspire                        V1, 2.1, 3,4,5,6,7,8   Consultant

Ian Atkinson             JCU                             V5,6,7,8               Research Director

Nigel Sim                JCU                             V7,8                   Product Manager

Russell Sim              JCU                             V7,8                   Systems Engineer

Lynn Alford              JCU                             V7,8                   Plone Developer


Document Profile
Filename                       Consultancy Proposal

Document Author                Andrew Alexander

Current Version                Version 8

Issue Date                     7/04/2008




Revision History
Date                       Version         Action – Description                         Author

2/02/2008                  V 1.0           Response Preparation                         Andrew Alexander

23/03/08                   V 2.1           Initial Customer Document Review             Dominique Gorse

2/03/08                    V3              Review                                       Frank Eilert, Dominique Gorse

14/03/08                   V4              Amend proposal                               Andrew Alexander, D Gorse

23/3/08                    V5.0            Publish Document for Submission              Andrew Alexander Frank Eilert,

27/03/08                   V6.0            Review of document                           Andrew Alexander

5/04/08                    V7.0            Draft                                        Andrew Alexander

7/04/08                    V8.0            Final Draft                                  Nigel & Russell Sim and Lynn Alford
Executive Summary

The solution that is contained in this document has been developed by ARCHER using “Open Source”
software to provide research groups with a low cost, secure and customizable solution for collaboration and
data management. The solution is designed to reduce the time taken by researchers to access secure
information, interact with fellow researchers and produce outcomes from their work. While this solution is
a comprehensive solution it is expected that it will continue to be developed and provide more
enhancements that will be leveraged by other researchers.

In particular there have been certain enhancements which ARCHER has developed that we believe will add
significant value to QFABS clients. These include the Plone “Cache Accelerator” (to speed up search &
screen speed), Forums (for collaboration), SRB Integration (for large file data storage), RSS feeds for
notification of content changes, task management and task allocation (for project Management), SRB iCat
metadata manager, Plone global search capability by metadata, author, title or body text, SSL Logins and
Plone iCal integration.

A number of the features requested by the National Breast Cancer research Group (NBCRG) were not able
to be integrated into Plone in the timeframe allocated for delivering this solution. It is hoped that we will be
able to provide further enhancements for QFAB and NBCRG in the future. We have listed some of the
future features (P22) which may be added upon further discussion and look forward to your views on this
document and what other services would add value to research outcomes.

Archer has been pleased to provide this solution for QFAB and its clients and support beyond ARCHER
will be provided by JCU, the details of which will require further discussion and an understanding of the
support required. It is envisaged that ARCHER will start to implement the solution on the 21st April 2008
and complete the installation, configuration and training by the 25th of April with the likelihood that QFAB
will go live with their client on April 30. We have allowed a month for client familiarization prior to a
project finalization in June that will include a discussion on future steps and ongoing requirements. We
look forward to the successful implementation of this project and would like to thank QFAB and the
NBCRG for their input and assistance.
                                                                                   CONTENTS

Executive Summary ......................................................................................................................................... 3
Overview.......................................................................................................................................................... 5
    ARCHER .....................................................................................................................................................................................5
    QFAB (The Customer) ................................................................................................................................................................5
    Overview National Breast Cancer Research Group (The Customer’s Customer) ........................................................................5
    Purpose of the Research Group ...................................................................................................................................................6
    Groups Objectives .......................................................................................................................................................................7
Project Scope ................................................................................................................................................... 7
General Requirements ..................................................................................................................................... 7
   General Roles and Responsibilities ..............................................................................................................................................8
   Overall Requirements Description ...............................................................................................................................................8
Testing Environment ..................................................................................................................................... 10
Assumptions .................................................................................................................................................. 10
User Documentation ...................................................................................................................................... 10
Support ........................................................................................................................................................... 11
Plone interface ............................................................................................................................................... 11
    Privacy/Security.........................................................................................................................................................................12
    Home Page .................................................................................................................................................................................12
    Plone Layout ..............................................................................................................................................................................13
    Folders Management .................................................................................................................................................................14
    Document Permissions ..............................................................................................................................................................14
    Publishing ..................................................................................................................................................................................15
    Comments ..................................................................................................................................................................................15
    Funding Partners ........................................................................................................................................................................16
    External members ......................................................................................................................................................................16
    Search ........................................................................................................................................................................................17
    Project Management ..................................................................................................................................................................17
    Discussion Forums ....................................................................................................................................................................18
    News & Events ..........................................................................................................................................................................18
    Help ...........................................................................................................................................................................................19
Roles and Access within the NBCF Plone .................................................................................................... 20
   QFAB Plone User structure by Role ..........................................................................................................................................20
   QFAB Plone Users .....................................................................................................................................................................20
   QFab Plone User Access Rights .................................................................................................................................................21
   Making Files Private ...................................................................................................................................................................21
   Plone Requirements ....................................................................................................................................................................22
Hardware Requirements ................................................................................................................................ 24
Authentication and Security .......................................................................................................................... 25
Data Capture, Storage & Management .......................................................................................................... 26
    Access Architecture: (see assumptions).....................................................................................................................................26
    Use Case for Collaboration and Data Management ...................................................................................................................27
    Proposed Data Management Use Case Structure .......................................................................................................................28
    iCAT Core Tables ......................................................................................................................................................................29
    Proposed SRB Data Structure ....................................................................................................................................................29
Implementation .............................................................................................................................................. 30
    SRB Implementation Steps ........................................................................................................................................................30
Training.......................................................................................................................................................... 31
    Plone Training ...........................................................................................................................................................................31
    SRB Training .............................................................................................................................................................................32
Proposed Future Projects ............................................................................................................................... 32
Summary ........................................................................................................................................................ 32
Proposal Signoff ............................................................................................................................................ 33
Overview

ARCHER

ARCHER is a project to productionise the software tools developed under the DART project and adapt
them to fit the needs of a number of NCRIS priority research capabilities. The ARCHER project has setup
dedicated task forces to analyse e Research data and information management needs and requirements,
taking special note of existing IT services available and applicable to each research area. Adapting the
generic DART middleware/software tools (developed from a previous e Research project) to suit each
research area, these dedicated task forces have further developed the tools to suit the needs of specific
areas, and where possible will incorporate them into customised research portals. Part of the ARCHER
project methodology will be to productionise these tools, through operational testing, usability and
reliability trials, so as to produce robust industrial-strength software tools. The DART & ARCHER
objectives are to improve the ability of researchers to:

        collect, capture and retain large data sets and streams from a range of different sources;
        deal with the infrastructural issues of scale, sustainability and interoperability between repositories;
        support deposit into, access to, and annotation by a range of actors, to a set of digital libraries which
         include publications, datasets, simulations, software and dynamic knowledge representations;
        assist researchers in dealing with intellectual property issues during the research process; and
        adopt next-generation methods for research publication, dissemination and access.



QFAB (The Customer)

       QFAB was recently established with funding from the Queensland State Government with matching funding
       from Partners to support various Bioscience research groups and enhance the State capability in
       Biotechnology. QFAB Partners are the University of Queensland, Institute for Molecular Biosciences (IMB),
       E-Health research, Griffith University, QUT, ARC centre for Bioinformatics, SRC in Functional & Applied
       Genomics, Queensland Department of Primary Industries and Queensland Cyber Infrastructure Foundation
       (QCIF, Australian Partnership in Advanced Computing. Partners provide resourcing such as people and
       knowledge, but QFAB only have a small core group of staff dedicated to the overall success of QFAB.
       They have recently been offered to provide the technology infrastructure & support for a new Breast Cancer
       research group which has been funded by the “National Breast Cancer Foundation” to the tune of $5m over
       5 years. This is a critical customer for QFAB as it will demonstrate to the wider research community QFAB’s
       ability to deliver specialist services. QFAB sees ARCHER able to provide collaboration tools and a data
       management platform suitable for its projects.



Overview National Breast Cancer Research Group (The Customer’s Customer)

       This is a group of clinical cancer researchers who are spread out across Australia but who have worked
       together on other projects successfully. This is a primary reason for funding of this project. While each group
       has specialist skills in various segments of cancer research, it is expected the multidisciplinary approach
       provided by this team will provide new and innovative derivations of Breast Cancer pathways. Their
    members are individually highly skilled and IT savvy but also time poor and lacking infrastructure to link
    them together. The primary leader and person who obtained the funding is Christine Clarke (Westmead
    Millennium Institute Sydney), she has strong personal relationships with all the other key group leaders
    including Mark Regan who is also participating in the research. The key members of each group have strong
    relationships with each other and are committed to working together; in fact George Muscat (a lead CI) has
    explained that a large reason for the groups success is their strong personal relationships and
    communication between the groups. He has indicated that collaboration is a key component of their
    requirement, not just between each other, but also to the wider community and to their funding partners.
    The project has started and the project manager, Elizabeth Kuczek, has been appointed to manage the
    project activity. Rick Kefford was appointed to head the “Clinical Advisory Group” with John Funder to head
    the “International Advisory Group”.




Purpose of the Research Group
    The research group will identify the Nuclear Receptor (NR) networks active in breast cancers, to identify new
    targets for treatment. Because the components of NR networks are so closely interlinked, their
    simultaneous evaluation will provide the power required to identify critical players in breast cancer biology.
    The knowledge will be translated within the granting period, through the application of treatments with
    existing NR ligands in women who have failed on endocrine or cytotoxic treatments. Beyond the scope of
    this funding period, new rational small molecule agents will be developed and tested in Phase 1/2/3 trials in
    currently underserved breast cancer subgroups.
    An integrated approach to information management is critical to this project, as indeed to any project
    involving high-throughput data generation at multiple sites, large complex data sets, computational
    inference and collaborative analysis. There will be four components of project bioinformatics:
    -       Management of data generated in project;
    -       Integration of project data with other information sources; extended ontologies;
    -       Data analysis including algorithms & software for pathways & network; and
    -       Support of collaboration in data generation, access and analysis.
    It is likely that many new analysis tools, datasets etc, will appear during the lifetime of this project,
    particularly in literature mining, high-throughput omic technologies including DNA resequencing, data
    integration, automated inferencing and network analysis.
    It is intended that QFAB will implement and manage all these technologies to support real-time
    collaboration in data analysis and knowledge discovery across all the project teams.
Groups Objectives
      Aim 1: 2008 To identify NRs, coregulators, and associated critical regulators in breast cancers.
      Aim 2: 2008 To refine the identified NR family members to select those most likely to be critical in cancer
      Aim 3: 2009-11 To identify targets of NR pathways in the breast
      Aim 4: 2009-11 To validate the role of critical NR pathway components in experimental models of cancer
      Aim 5: 2011 To identify NR pathway components with predictive power in breast cancer
      Aim 6: 2012 To develop new breast cancer treatments by targeting NR pathways




Project Scope
The software will provide an interface to facilitate communication and collaboration between members of the
research group, their funding partners and international and national collaborators. It will also provide a means to
capture, interrogate and manage data used in their research. The data consists of text based documents, statistical
information, images and laboratory information. The interface will provide the user with the ability to access
different applications, data and information in a secure environment.




General Requirements
The NBCF project group needs will address the following specific areas/fields:
    Collaborative Workspaces
    Data Collection and Management
General Roles and Responsibilities

        Below are the roles and responsibilities for product/software tools that are deployed.




      Life Cycle         Role                                              Responsibility
      Planning           Setup hardware for Development                    Development Team- Russell Sim
                         Functional Specs                                  Dominique Gorse & Andrew Alexander
                         Detailed Design                                   Development Team – Lynn Alford & Nigel Sim
                         Test Design                                       System Test Lead – Nigel Sim/Russell Sim
                         Development Project Plan                          Development Team A Alexander/Frank Eilert
                         Test Project Plan and Budget                      Development Team A Alexander/Frank Eilert
                         Overall Project Plan                              Account Manager Andrew Alexander
      Construction       Coding                                            Development Team – Lynn Alford & Nigel Sim
                         Unit Testing                                      Customer – Dominique Gorse
                         System Test - Test Cases                          System Test Team- Russell Sim
                         User Test – User Test Lead                        Customer – Dominique Gorse
                         User Test - Test Cases                            Customer – Dominique Gorse
                         Setup hardware for System Testing                 System Test Team – Russell Sim
      System Testing     Migration of code/database from                   Development Team – Nigel Sim & Russell Sim
                         Development to System Test
                         Populate test database for System Test            Development Team – Russell Sim
                         System Testing                                    System Test Team – Dominique Gorse &
                                                                           Russell Sim
                         Bug Tracking / Triage                             Russell Sim, Lynn Alford and Nigel Sim
      User               Migration of code from System Test to UAT         Development Team- Russell Sim
      Acceptance Test
                         Populate test database for UAT                    Customer – Dominique Gorse
                         UAT Testing                                       Customer – Dominique Gorse
                         Bug Tracking / Triage                             System Test Lead, DM, PM, User Test Lead
      Production         Migration of code from UAT to Production                 Customer – Dominique Gorse
      Training           Training QFAB Staff in System Maintenance         Development Team – Lynn Alford, Russell Sim
                                                                                           & Nigel Sim
      Training           Training NBCR Customer in System Use                     Customer – Dominique Gorse
      Help Files         Develop Help files for user support                    Development Team- Dianna Hardy




Overall Requirements Description

The solution required consists of two integrated elements, firstly a web based collaboration portal for
communication and review of information and secondly a storage and management application for research data.
It has been decide to use “Plone” to provide the collaboration portal and SRB to provide the data management. It is
envisaged that this initial deployment will be incrementally improved over time to deliver a more comprehensive
interface between researchers and their work, thereby improving the outcomes of that work. The below diagram is
provided to depict the activities required by researchers in this initial solution.
1.P




3.O
Testing Environment
All testing will initially be manually performed to ensure front-end performance and suitability to
requirements is achieved while back-end performance will be tested in QFAB under load situations to
ensure reliability requirements have been met. The system will be created first at JCU where it can have
initial performance testing provided under controlled conditions. This will then be packaged as a complete
system for deployment at QFAB so that issues faced during deployment will mainly be hardware related


Assumptions
In moving forward to meet requirements, it is necessary to frame the work and provide some assumptions
that the work provided is dependant and will be based on:-
    1. The operating environment will structured around the following
         Linux as the server operating system; the version of Linux to be determined later
         MySQL as the server database (also targeting compatibility with Oracle, where required)
         Apache as the web server
         Tomcat as the application server
         Java as the default development language to maximise platform independence
         OS-agnostic client platform (i.e. Windows, Mac O/S or Linux).
   2. Users’ institutions will be members of the Australian Higher Education and Research Trust
      Federation [now called the AAF]. Tools developed will support Shibboleth (where required) but
      this is dependent upon AAF accepting Shibboleth as a standard for security certificate provision
      across institutions.
   3. Software will be developed to support the Windows XP, Macintosh V10 and current Linux desktop
      environments (as at 1/4/08).
   4. User testing rather than testing tools will be employed predominantly due to the low level of new
      code development required by the Archer team.




User Documentation
            The system shall provide an online hierarchical and cross-linked help system that describes
             and illustrates most if not all system functions.
            These help files will be generic and not specific to QFAB
            FAQ is a forum which enables users to post questions to support that will be answered in time
             and not immediately. It is designed to help formulate specific help subjects and not to be a
             turnkey help section with preformatted material.
            The system shall provide an online tutorial to allow users to familiarize themselves with the
             operation of the system using a static tutorial menu.
Support
It is envisaged that QFAB will provide 1st and 2nd Level technical support to the members of the NBCRG,
this will include answering user queries and providing training where required. Support will be provided by
ARCHER to QFAB on both a technical and developmental level up to the 30/6/2008, after that point
formal support arrangements should be negotiated with JCU to deliver 3rd level technical support and
further development assistance in Plone or SRB. Both applications are “Open Source” products and web
site resources are also available @ www.plone.org and www.sdsc.edu/srb/index.php/Main_Page.


Plone interface
The Collaborative workspace application for the members of the NBCF project has been developed using
“Plone”. This product provides a number of benefits; open source (free), easy customisation, acceptance
within the research community, scalability (1-10,000 users) and ability to integrate with other tools that
provide a single point of use for research activities. Some proposed functional layouts are detailed below.

                                                                                                 Funding                     Members                      All see &                Central       Right Hand       Left Hand
Plone Functional Appearance- QFAB All                                                            Members                     only will                      have                   Frame           Frame           Frame
                                                                                                   only                        see                         access
  Sub Menus




                                                                                                                                                  Aim 1
                         Members                                                    Members                        Admin                                                                                   Contents
                                                       News                                                                                       Aim 2
                           Login/                                                    Forum                        Meetings                                                     Budget                       Search
                                                                                                                                                  Aim 3
                          Logout                                                                                   To Do                                                                                    How to
                                                       Events                                                                                     Aim 4
                        Preferences                                                  Public                       Reports                                                     Reports                       Videos
                                                                                                                                                  Aim 5
                         My Folder                                                   Forum                                                                                                                   FAQ
                                                                                                                                                  Aim6
Menu Title
  Tabs




                                                 Events/                       Discussion                    Project                                                                           Funding
                      HOME                        News                                                                                     Research                   Literature                                      Help
                                                                                 Forum                     Management                                                                          Reports
Navigation
Windows




                      Personal                                                                              Tagged for                                                                          Project
                                                                 Upcoming                                                                                                                                          Help &
                     options as           Navigation                                   Recent               Attention or                                Folder               Forum            Management/
                                                                 Calendar/                                                          Search                                                                          Online
                     Horizontal           Side Menu                                   Changes                message                                  management           Management            ticket
                                                                Events/News                                                                                                                                        Training
                   text links only                                                                             board                                                                          management




                   By default will                               By default will     Will Appear in                                                                                          Only appears in
                                                                                                                                  Will appear                           By default will
  Location




                appear under main        Will Appear in           appear in left     all screens on        By default will                            By default                               center frame     Only appears
                                                                                                                                  on all pages                        only appear when
                 tabs , right hand       all screens on           frame except        lft hand side          appear in                                will appear                            with HOME and       when Help is
                                                                                                                                   in top right                           forums are
                 side in horizontal       lft hand side         when events are            after            center frame                               in center                                then in right    selected and
                                                                                                                                  hand corner                         selected and then
                     text links                                 selected directly      Navigation          for home only                                 frame                                frame with My     then in center
                                                                                                                                    of screen                          in center frame
                                                                 then in centre                                                                                                                    folder           frame



                                                                                                                                               Provide a capability     Provide a venue for        Provide Task
                                                                                                                         Provide a capability                                                      allocation and
                                                           Provide an overview                       Provide a summary                         to open, edit, delete      discussing data,
                 Provides links to                                                      Provide a                              to search                                                             tracking by
                                                                of important                             of important                         or manage files. Can           events and                               Provide a
               preferences, team     Provide an overview                         summary of recent                       documents either by                                                        milestone or
                                                          information published                       information which                         customise access      information which can                         catalogue of
               members, contact and catorgorisation of                            changes made to                          word or phrase,                                                           project and
  Function




                                                                as news and                          has been tagged by                        rights or review and    be kept for member                                help
               details, picture and      information                                 files that are                          through title,                                                      include workflow
                                                            upcoming and past                         othermembers to                         publish these files for       access only,                             information
                 other information   associated with the                         associated with the                         metadata or                                                           (Kepler), and
                                                              events as well as                      be read by the user                          general access.          highlighted for                        including, wink
               including personal       main frame eg                              user including,                         contents located                                                         reporting on
                                                              personal meeting                        including, news or                       Ownership rights by member comment or                              video, images,
              files (my folder) and documents, calendar,                                 news or                            within the zope                                                             project
                                                           scheduled which will                       documents, forum                           default will allow    published for access                       documents and
              profile and password    tasks, folders etc.                           documents or                          database eg word                                                        completion and
                                                          have links to relevant                        discussions or                          other members to         and comment by                                 FAQ.
                  management.                                                          comments                           documents, PDF                                                             minutes or
                                                           files eg agendas etc                           comments                               access and leave       funding partners or
                                                                                                                                  etc.                                                              agendas for
                                                                                                                                                comments on files          collaborators.
                                                                                                                                                                                                      meetings
Privacy/Security

The solution that has been provided has a number of layers of security which ensure that data and
information that is located in your portal is secure. The primary safeguard is that only people with a user
name and password supplied by you can access the site. Then you can assign access rights to those that
have been given access, this enables you to control the access to information. (by default all members of
research teams will have access to all member information.)




Home Page

This is designed to bring the most relevant information to the member when they login. The system will
enable others to tag files with a specific metadata tag that will be read by the system and collected for
display to the relevant parties. It will also (but not displayed) provide the tasks allocated to the member in
order of urgency so that they can plan their daily activities.
Plone Layout
Various sections can be accessed via the links and navigation horizontal bar:

Top links
    My Folder
           o    Private area for each users
      My Dashboard
           o    Includes to-do list
           o    Recent Changes
      Site Map
      Accessibility
      Contact Site Support
      Log out
      Site Setup (for administrator)
           o    Users, access, permissions…

Horizontal bar menu
    Home
           o    Private area for each users
           o    Includes to-do list
           o    Includes tagged (important information) files
           o    Recent News, recent changes
      Events
           o    Events- ability to write or tag for attention of all members
      News
           o    News – ability to write or tag for attention of all members
      Discussion Forum
           o    Discussion on various topics by member only
           o    Separate discussion forum by member, collaborator and partner
           o    Capability to publish member only forum to collaborator/partner forum
      Project Management
           o    Meetings including minutes & agenda
           o    Assign Tasks & review progress
           o    Milestones & Task assignment (To-Do List)
           o    Reports
           o    Ethics
      Research
           o    Aim 1 to Aim 6
      Literature
           o    Repository for papers relevant to the project.
      Funding Reports
           o    Budget
           o    Reports
      Help
           o    Index of help topics
           o    Wink Videos on how to perform tasks
           o    “How to” Documents
           o    Images and screen shots
           o    FAQ
Folders Management

Hierarchical display of folders allows grouping of information and sharing or publishing by individual file
or directory. By default access has been granted to members for all files but not those external to the group.
Members should be aware that when saving a file to the site they must change permissions to if they don’t
want others to be able to review or edit the file.




Document Permissions

Below can be seen the changes to permissions which can be made to any file or directory created by a
member. The document owner has default rights but these rights are also shared by administrators. The
owner has the sole rights to publish their files for viewing by those people outside the group (include
funding partners or external researchers). However any publishing of document must be authorised by
either a reviewer or administrator.
Publishing
In the first screenshot of “Folder Management” there is a selection under “logout” that is marked Private
(in red). If you select this and choose “Advanced” from the drop down box you will get the screen below.
This is where a document is submitted for publication, it also allows you to set a time-limit on publication
and also comments to justify or detail more information to the reviewer. Once approved this document will
still be available to normal members but will also appear in the navigation areas of external researchers.




Comments

Members will also be able to comment on documents and those comments will be associated with each file
in chronological order, creating an add hoc forum specifically related to the document in question.
Funding Partners

The importance of funding partners has been recognised in this system where a separate category of user
has been defined to enable “Funding Partner” to access a private area where project reports and financial
information can be disseminated and monitored. This group will also have access to published material and
news and events. It is suggested that another site be developed that is an outward facing site and doesn’t
require any login. This site will be designed to market the activity of the research group and also give
exposure to the funding by the NBCF.


Picture of Funding Partner window here



External members

This is made up of members of the International Advisory Group and the National Clinical Advisory Group
and except for John Funder and Rick Kefford they are not part of the research group and will have access
to limited resources as published by the group from time to time. These resources will include “Literature”,
“News”, “Events”, and “Public Discussion Forums”.

Picture of External screen here
Search
Search is capable in both Plone and SRB as Plone caches the metadata from SRB, this search capability has
3 options. The first is a “live search” which reacts to the text typed in the search box, the second is an
advanced search that enables search by metadata tag or category and is selected at the bottom of the “live
search window” and the third is to search only in the current section you are in. Searches will only return
files which you are authorised to view.




Project Management

Project Management uses the same folder management system as previously mentioned but also includes a
new component for task management and task assignment. This enable you to set up a project/milestone as
a new “action item list” and then you can add action items to that list for specific tasks with specific tags,
start date and finish date, notes and assign this by ownership to a member. This task will then appear in the
members task lists and personal folder for attention. You can then track the progress of action items
required for each action list.
Discussion Forums

Discussion Forums enable members to interact of specific subjects or issues, the forums are broken in to
two sections, Members forums for research members only and Collaborators Forums for external users to
engage in debate and assist members with particular issues. The forums will need to be managed closely if
they are to be useful as people only contribute when the subject matter and debate is lively but does not
evolve into personal abuse. It is suggested that firm usage policies be applied to all participants and
moderation of content is provided daily.




The forum also has its own search function which enables the member to search for specific text, recent
activity or unanswered posts. Forums have been modified to enable RSS feeds (notification of new entries
by email) and also metadata tags can be inserted so that new entries will also appear in tagged files when
the user logs in. (urgent info required to be viewed by other members).


News & Events

Events calendar enables project leaders to schedule important events in the portal, this can then be
transferred through to your outlook calendar through iCal.
News operates much like a folder item and can be added from any view under the add item “News Item”,
this item can also be published so that it can be viewed by external researchers.




Help
Generic Help documents and user training videos will be provided and inbuilt into the interface as
subfolders of help. A FAQ (frequently asked questions) folder (forum) will also be included but not
populated with material. This is so that QFAB can provide a forum based feedback to users and through the
forum, common questions can be identified and answered through searching the forum.
Roles and Access within the NBCF Plone

QFAB Plone User structure by Role

Users will be broken up into the following groups
   1. External Members:- This group will have access to documents, participate in public forums and view other
       information published by members. They will also be able to see news, events and calendar entries as well
       as view any general literature which may be available to members. This group will consist of the Clinical
       Advisory Group and International Advisory Committee. This group will be managed by John Funder and
       Richard Kefford as Reviewers.
   2. Funding Partners:- This group of people will be made up of Christine Clarke, NBCF project manager and
       other people from funding agencies as directed. This group will be managed by Christine Clarke and the
       Research Group Project Manager (TBA) as Reviewers.
   3. Research Members:- This group will consist of all other research people involved in the project and will not
       be broken down into further groups. Supervisory rights will be assigned to each CI assigned to different
       sites. This group will be managed by the Research Group Project Manager (TBA) and CI’s as Reviewers.
   4. Reviewers:- This group will be made up of supervisors and CI’s allocated to the research project. They will
       be able to approve publication of documents, delete data/documents and otherwise determine the
       visibility of information.
   5. Administrators:- This is a restricted group made up of primarily the IT administrator and possibly one other


QFAB Plone Users

     Western Australian Institute                             Institute for Molecular                       Facilities & Resources
        for Medical Research                                        Bioscience                      •Core facility containing multiple
    Professor Peter Leedman: CI                         Professor George Muscat : CI                Applied Biosystems 7900HT qPCR
    Dr Shane Colley                                     Dr Gary Leong                               instruments
    Dr Keith Giles                                      Dr Stephen Myers                            •High end imaging facility
    Dr Andrew Redfern                                                                               •Facilities for production of synthetic
    Dr Ben Wood                                                                                     molecules
                                                                                                    •Illumina microarray platform
                                                                                                                                                     International Advisory
          Facilities & Resources                                                                                           QFAB                      Committee
                                                            Northern Territory
     •Illumina microarray platform                                                                              Professor Mark Ragan: CI             Chair - Professor John Funder
     •Dual Mass-Spec Machines                                                                                   Mr Jeremy Barker
     •State-of-the-art mouse facility                                                                           Dr Dominique Gorse                   Professor Bert O’Malley
                                                                                        Queensland
     •Breast Cancer Tissue                  Western                                                                                                  Professor Edison Liu
     Microarray                             Australia                                                            ARC Centre for Excellence           Professor Mitch Dowsett
                                                                                                                     in Bioinformatics
                                                             South Australia                                    Professor Mark Ragan: CI             Professor David Huntsman
                                                                                                                                                     Professor Malcolm Pike
                                                                                                           Westmead Millennium Inst itute            Professor Frank Gannon
                                                                                            New           A/Professor Christine Clarke: CI
                                                                                           South          Professor Richard Kefford
                                                                                           Wales          Dr Patricia Mote                           National Clinical Advisory Group
           Hanson Institute                                                                               Dr Rosemary Balleine
     Dame Roma Mitchell Cancer                                                                        ACT Dr Dinny Graham                            Chair- Professor Richard Kefford
        Research Laboratories
                                                                                                                                                     Dr Rosemary Balleine
    Professor Wayne Tilley: CI                                                      Victoria
    Dr Lisa Butler                                                                                                  Facilities & Resources           Dr Andrew Redfern
                                                  Prince Henry’s Inst itute
    Dr Stephen N. Birrell                                                                                     •Digital tumour imaging
                                              Professor John Funder: CI                                                                              Dr Ben Wood
    Dr T Bianco-Miotto                                                                                        •Laser capture microdissection
                                              Professor Peter Fuller: CI
    Dr G Buchanan                                                                                             microscope                             Mr Stewart Hart
                                              Professor Evan Simpson: CI
    Dr T Hickey                                                                                               •Facility for culture and analysis
                                              Dr Colin Clyne                                                                                         Dr Stephen N. Birrell
                                                                                         Tasmania             of human tissue
                                              Dr Tim Cole
                                                                                                              •Image analysis                        Dr Gary Leong
                                              Dr Morag Young
        Facilities & Resources                                                                                •Illumina microarray platform
    •Image analysis                           Mr. Stewart Har t                                               •Facility for collecting, processing
    •Laser capture microdissection                                                                            and storage of clinical tissues
    microscope                                     Facilities & Resources
    •Facility for culture and analysis        •Core facility containing Applied
    of human tissue                           Biosystems 7900HT qPCR and
                                              DNA sequencing
                                                                                                         Australian Regenerative
                                              •Micro RNA analyses
                                                                                                        Medicine Institute (ARMI)
                                                                                                      Prof Nadia Rosenthal: CI

                                                                                                           Facilities & Resources
                                                                                                      •Generation of genetically
                                                                                                      modified mice
                                                                                                      •Access to EMBL mice including
                                         Collaborative Breast Cancer Research Grant                   international consortia
  QFab Plone User Access Rights

                                                               Projects
                                                  NEWS         (broken                      Forum &
                    Plone            Project      Event and    down     into   Published    Discussion
                    administration   Management   Meetings     AIMS)           Literature   area         REPORTS
Principal      CI
Christine Clarke                     RWAD         RWAD         RWAD            RWAD         RWAD         RWAD
IT Administrator    RWAD             RWAD         RWAD         RWAD            RWAD         RWAD         RWAD
Project manager                      RWAD         RWAD         RWAD            RWAD         RWAD         RWAD
Chief
Investigators                        RWAD         RWA          RWAD            RWA          RWA
Researchers
participating in
the project                          RW           RWAD         RWAD            RWAD         RWAD
International
Advisory
Committee                                         R                            RWA          RWA

National Clinical
Advisory Group                                    R                            RWA          RWA
NBCF                                 R            R                            R                         RWA
R=                  Read             W=           Write        A=              Add          D=           Delete/Move

  By default all information is shared for authorised roles and with the ability to add comments, except for
  the “My Folder” which is private by default.

   Making Files Private

  By default all files will be visible to other members. To set a file or folder to private untick the “Inherit
  permissions from higher levels”




  Note that in the sharing tab, we have ticked the box to inherit permissions from higher levels. If you untick the box,
  sharing with all logged in users is no longer allowed, therefore the document or folder can become private to the
  owner.
Plone Requirements

These requirements have been stack ranked by feature with the lowest stack rank being most important and the
highest stack rank being least important. This will allow any development team to prioritise important items and
enable effective development that is most likely to meet timeline expectations. It is envisaged that items ranked as 1
will be delivered in the initial deployment and items ranked as 2 or higher will be progressively introduced after
further research, approval by QFAB and will require separate development proposals.


            Category           Rank     Feature’s already part of Plone that needs testing
            Document
            Management
                               1        File Distribution capability by group or member.
                               1        Workflow Engine for publishing information/documents
                               1        Metadata Entry and search capability
                               1        Basic and Advanced search capability of metadata and content
                               1        User Contribution management & document publishing control
                               1        My Page / Dashboard
            Security/User
            Access
                               1        Audit Trail of access to site and document changes
                               1        Content Approval
                               1        Granular Privileges
                               1        LDAP Authentication
                               1        Sandbox for testing
                               1        SSL Compatible interface
                               1        Versioning control
                               1        Extensible User Profiles
           Content
           Management
                               1        Clipboard for cut and paste
                               1        Content Scheduling
                               1        Inline Administration
                               1        Online Administration
                               1        Package Deployment
                               1        Sub-sites / Roots
                               1        Customisable Themes / Skins
                               1        Web-based Style/Template Management
                               1        Web-based Translation Management
                               1        Link Management
                               1        Blogs
                               1        Site Map
                               1        Events Calendar
                               1        Events Management
                               1        Interface Localization
                               1        Drag-N-Drop Content
                               1        Multi-Site Deployment capability
                               1        URL Rewriting functionality
                               1        CGI-mode Support
                               1        Content Reuse
                               1        Friendly URLs
                               1        Image Resizing
                               1        Macro Language
                               1        Mass Upload
                               1        Prototyping
                               1        Server Page Language
                               1        Site Setup Wizard
                               1        Online Help
                   1     Email Verification of changes or additions to documents/forums
Interoperability
                   1     FTP Support
                   1     UTF-8 Support
                   1     WAI Compliant
                   1     WebDAV Support
                   1     XHTML Compliant
                   1     Advanced Caching
                   1     Database Replication
                   1     Load Balancing
                   1     Page Caching
                   1     Web Services Front End
Category           Req   Requirements which require further development
Content
Management
                   1     RSS Feeds to attach to Forums & Documents
                   1     Static Content Export to reduce overhead when loading
                   1     Discussion Forums by group permission
                   1     Ability to Publish forums for public access
                   2     Tag files/events/forums for special collection and display as
                         important
                   2     Mail Form – form that can send a message to specific address
                   1     iCal compatibility and integration
User & Access
Management
                   1     SSL Logins
                   3     Pluggable Authentication - Shibboleth
                   3     Login History
                   3     Address Book and Contact manager
Document     &     1.0
Communication
Management
                   2     Email to members re changes to discussion forum
                   3     Spell Checker for text fields
                   3     Add Instant message chat capability and presence awareness of
                         members
                   2     Data Entry from experimental systems
Help
Management
                   3     FAQ Management
                   2     Wink Videos for tutorials
Interoperability   1.0
                   3     Integrate Endnote into Plone
                   2     Integrate with SRB Data Management system
                   2     Integrate Project Milestone and task manager
Hardware Requirements
Below is a diagram depicting the hardware requirements to run the proposed solution at QFAB. Preferred
server platform is Red Hat Ver5. Secondary network cards will be used to create a private network between
virtual machines that will not have access to the outside world. This will enable systems to communicate
between the DMZ and the Public Network without causing an issue with exposed systems. (see below)



                                                                                                   2G ram
                                                                                                   10G
                                                                 user                              storage
     512 ram                                                                  Public
                                 Public                           Ports
     10G storage     Ports
                                                                  Incoming: 80, 443
                     Incoming: 5544, 80, 443
                                                                  Outgoing: & Public
     Delete SRB-PROD Outgoing: &
     Create SRB                                                                         WPLONE
                      SRB                SRB                             Httpd
                         MyProxy                                    Cache(varnish)
                                                                    Httpd
                         Globus                                     Cache(varnish)
                         iCat

                                   Private                        Ports      Private
                                                                             Private
                        Ports
                        Incoming: 5544, 80, 443           DMZ     Incoming:
                                                                  Outgoing:8080
                        Outgoing: 5544, 5432
                                                                                                   System
                                            Private direct IP                                      Backup
                                              connections                                          32 Bit
                                                                                                   Redhat 5
              512 ram             Private                                     Private
                        Ports                                     Ports
                        Incoming: 5432,5544                       Incoming: 8080          1G ram
                        Outgoing: 5544                            Outgoing: 80,443
                                                                                        PLONE
                                               SRBDB
                                                                         Plone
                           SRB Fileserver
                                                                         (zope)
                            PostgreSQL                                             Fiber Channel


                                       Fiber channel mount SAN          Fiber channel mount SAN

                                              100G storage                                  100G storage
                                              BACKUP                                        BACKUP
                                                                         Zope DB



      QFAB Production Network
Authentication and Security
User will be initially authenticated by QFAB LDAP where relevant user authentication will be provided. If
the member’s institutions are part of the Australian Access Federation, federated authentication might be
implemented in a later stage. This is most likely to be delivered by Shibboleth, but is reliant upon the
Australian Access federation being accepted as a standard by all institutions.

The Plone and associated data will be hosted on the QFAB DMZ. Confidentiality of the data will rely on
the application security and robustness.
.

      Communication over the internet to the Plone and other applications will be run over SSL with the
       use of certificates.
      Data will be stored on the IMB Hierarchical Storage Management and backups will be performed
       daily.
      Archival of aim specific data will be performed at the end of each Aim.
Data Capture, Storage & Management
QFAB will need to provide a way to ingest various files in different formats into a data management
system. These files will initially be located at IMB but may later be located in multiple locations, certainly
other clients will have differing requirements and so a flexible data management system will be required.
Required features include:-

       1.  Ability to deposit a single file or object into the collaboration system
       2.  Ability to submit multiple files or delete files or objects (batch system)
       3.  Support for a range of standard data formats
       4.  Compliance with the needs of the iCAT Metadata Management system
       5.  Ability to transfer or process large data sets via GRID Technologies.
       6.  Ability to store or access large or small data sets in diverse locations securely
       7.  Access control to ensure only research team members or other authorised persons have read or
           write access
       8. Secure and reliable software system
       9. Ability to cope with very large objects or files
       10. User-friendly interface either as an integrated system or as a separate data management
           interface


The data management system (SRB) will integrate with Plone which will cache the metadata tables. This
will enable researchers to search the collaboration portal for documents located in SRB. SRB will become
a directory structure visible from Plone but will not be the transport or copying mechanism for SRB. That
will be done from SRB through a desktop interface (“Hermes” or Grid FTP).



Access Architecture: (see assumptions)
            -   Operating system Desktop is WinTel (Windows XP) or Macintosh (ver10.3) or Linux (Red
                Hat)
            -   Database – PGSQL & Zope
            -   Server Environment is running on Linux or WinTel servers
            -   Hermes Client (Windows and Mac)
            -   Web Interface for Plone (IE6 or Firefox)
            -   Login based on QFAB LDAP
            -   Data & Metadata management by SRB
Use Case for Collaboration and Data Management

The diagram below depict the functional activities that can be provided with the solution provided




                                                                                                     1.



                                                                                                     7
        Administrator
Proposed Data Management Use Case Structure

The version of SRB will provide the following functions and capabilities for data management




                                        Project




                                                                                         Experim
iCAT Core Tables

The SRB MCAT has been enhanced by the ARCHER team to include the iCAT metadata storage and
management module. This provides for a more robust system and speeds data access and metadata
management. The following data structure will be provided with the instance of SRB.

                                                      PROJECT




                                                   PROJECTEXPERI
                                                                       INVESTIGATOR
                                                       MENT




                                PUBLICATION

                                                    EXPERIMENT            SAMPLE


                                 KEYWORDS



                                                      DATASET

                                 TOPICLIST




                                                      DATAFILE




                                  iCAT metadata core tables for Crystallography v0.3




                                       iCAT Metadata Core Tables


Proposed SRB Data Structure




            iCAT tables v0.2 (with some
             column renaming by BobC)
Implementation
The implementation will be provided by the ARCHER team and will be performed within the QFAB
network and on QFAB servers. The implementation is planned for the 21st of April and subject to this
document receiving signoff by QFAB and their customer prior to the 21st. It is anticipated that the
implementation of software and configuration of hardware will take approximately 3 days with 1 day for
system and maintenance training. A further day has been allocated for Plone administration and
customisation training which planned to be carried out on Friday the 25th of April. After a further week of
testing and customisation the system should be ready to go live with the NBCRG on 30th .

Plone Implementation Steps (David to do)

Deployment of customized Plone for NBCF onto QFAB server
Train QFAB on Plone administration
    Maintenance and Backup
    Database access and administration (Zope)
    Changing/controlling permissions



SRB Implementation Steps
      Install VDT to provide Globus and MyProxy (/opt/vdt)
      Test cert generation against LDAP (LDAP provided?)
      Generate SRB certificate,
      Identify the location of the SRB storage. Perhaps this can be a
      symlinked so it can move in future.
      Identify the SRB zone and domain names
      Unpack the SRB install and configure it with the above domain, zone,
      certificate and vault
      Test connection with an SRB admin account
      Test connection with LDAP user from Hermes
      Configure Hermes template connection for deployment.
      Install Tomcat (or check provided installation)
      Configure and deploy MCATExt WAR file
      Check web services becomes available
      Configure and deploy ICAT WAR file
      Check web service becomes available
      Check ICAT registers with MCATExt
      Install Plone ICAT product
      Test Plone ICAT connects to ICAT and SRB
Staff providing the implementation will do so alongside QFAB staff to ensure that knowledge transfer
takes place.

Date       Person          Task                                      QFab Requirement
21/4/08    Russell Sim     Install Plone servers into QFab &         Provide 2 staff, Red Hat V5
                           configure with network                    Configured Servers as per spec &
                                                                     network support
21/4/08    Nigel Sim       Install SRB servers into QFab &           Provide 2 staff, Red Hat V5
                           configure with network                    Configured Servers as per spec &
                                                                     network support
22/4/08    Nigel &         Complete install of Plone and SRB         Provide 2 staff, Red Hat V5
           Russell Sim     on QFab servers                           Configured Servers as per spec &
                                                                     network support
23/4/08    Nigel &         Test servers and links between            Access to network resources and
           Russell Sim     SRB and Plone as well as                  desktops for testing the system
                           performance and functionality in
                           the QFAB environment
24/4/08    Nigel and       Provide maintenance training on           Provide 2 staff and suitable
           Russell Sim     Plone and SRB system and                  situation for training on a one on
                           administrator and user training on        one basis
                           SRB and Hermes
25/4/08    Lynne           Provide administration and                Provide at least 2 staff, suitable
                           customisation training on Plone           quiet room, projector or large
                                                                     screen PC with access to the
                                                                     Plone instance at QFAB.




Training
Training will be conducted in QFAB premises using equipment provided by QFAB, ARCHER will supply
the staff to conduct administrative training and system training during the implementation. The planned
training will not include hand outs or any other written material as this doesn’t exist. Trainees will be
expected to take notes and ask questions about any aspect where they require further information. It is
planned that systems training will be conducted one on one during the system implementation and
administration training will be conducted after the implementation.


Plone Training

Plone training for administration will be provided by ARCHER, the elements that will be covered include:-

      Basics of the Plone environment
      Review of the Plone Control Panel
       - Adding tabs
       - Changing layout
       - Adding plug-ins
      Users and Groups - adding users, removing users, maintaining groups
      Security model of Plone - how the access to files and folders is controlled
      Portlets - how they work in the plone environment
SRB Training

The following elements will be covered in administrator training for SRB, these include :-
    Understanding of SRB environment
    Globus environment variables
    Server and CA certificates and locations
    Vault location
    Log and configuration locations
    Managing SRB resources (adding)
    Testing connections from the command line
    Debugging SRB issues
    Common error codes and their meanings (website will be provided)
    Maintenance of DB
    MyProxy configuration
    Debugging MyProxy issues


Proposed Future Projects
We recognise that your wish list for features was longer than what we have been able to provide
immediately. This was primarily due to the lack of resources to provide development within the timeframe
we had for deployment. We would however like to discuss these other elements to quantify their value to
the group and our ability to deliver them. These will be treated as separate projects and included:-
       Sharing address books and contact details in Plone
       Embedding Endnote or other annotation program within Plone
       Provision of a Metadata editor for Plone (to change metadata by folder not just file)
       Integrated permissions from Plone to SRB (ie change permissions in plone and that changes
          permissions in SRB)
       Drag and drop file management within Plone
       Skype or other Video/Voice conference capability imbedded or activated from Plone
       Create multiple looks of Plone so members can customise their desktop
       Customising Workflow application for web access within Plone
       Enhancements to Project Management (Action List)
       Public Facing site similar to http://plone.jcu.edu.au/eresearch



Summary
The solution that has been developed for QFAB and its customers is an integrated secure solution which is
designed to reduce the time taken for researchers to interact with information, other researchers or
complete tasks. It will be necessary for each research group to invest in keeping the site interesting by
monitoring content and providing reasons for members to access the site on a daily basis. We believe that
this iteration of the solution is only the first part to a greater solution which will be made available to other
researchers and we thank QFAB and the NBCRG for their input and assistance in this project.
Proposal Signoff
It is agreed between QFAB and The ARCHER Development Team


That the above proposal has been read and reviewed by the relevant and authorised persons below,
            shows that the proposal provides a clear understanding of the requirements of the work
              required, and that will be provided
            clearly outlines the responsibility requirements and deliverables.
                  th
Dated this   16        day of   April          2008




             _________________________         _________________________
             Signed by Ian Atkinson for and    Signed by Jeremy Barker for and on
             on behalf of the ARCHER           behalf of QFAB
             Project



             _________________________         _________________________
             Signed by the Development         Signed by the QFAB Technical
             group Project Manager             Director
             Frank Eilert                      Dominique Gorse

								
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