THE INFORMATION BELOW MARKED * AND [ ] HAS BEEN OMITTED PURSUANT TO A
REQUEST FOR CONFIDENTIAL TREATMENT. THE OMITTED PORTIONS HAVE BEEN
SEPARATELY FILED WITH THE COMMISSION.
PROGENITOR-PANGEA COLLABORATION AGREEMENT
INTRODUCTION
This document summarizes several discussions that have taken place between
Pangea and Progenitor relating to a potential collaboration between our
companies. It is our intention that this document serve as a framework under
which such collaboration will be guided and our mutual interests defined.
It is recognized by both parties that Pangea possesses certain technologies,
expertise, skills, and capabilities in bioinformatics, computing, data analysis
and handling, and that Progenitor possesses certain knowledge, expertise and
skills in the generation, interpretation and application of genomic information
and that a collaboration between the companies lead to a mutually beneficial and
synergistic arrangement.
In addition, both parties desire to collaborate to incorporate the knowledge and
skills of each in the conceptualization, development, and enhancement of
bioinformatics systems, software, and applications and in the use of these
systems, software and applications to make breakthroughs in drug discovery
research.
AREAS OF COLLABORATION
There are five areas of potential collaboration:
- Enhancing the existing functionality within GeneWorld-TM- and
Pangeanetics-TM-.
- Developing a relational database of genomic information. Pangea is
currently developing such a product (GeneThesaurus-TM-) -- that displays
and integrates genomic information in a relational format. It is
envisioned that, subject to mutual agreement, Progenitor will be
actively involved in determining the specifications for GeneThesaurus
and, in return, will be offered the opportunity to participate as a beta
test site for planned releases of the generally commercially available
versions of this software product no later than other beta test site
customers and will be offered the opportunity to license such versions
as soon as they become commercially available.
Pangea is planning to include model organism information (Menagerie-TM-)
in such a database. If Progenitor desires this additional functionality
to be available more quickly than scheduled by Pangea, then, subject to
mutual agreement, Pangea will assign software engineers to accomplish
this project by an agreed-upon date, and Progenitor will provide funding
for the project on mutually agreed terms.
- Validation of protein structure and function prediction tools may also
be an area of interest to Progenitor and Pangea. Pangea is currently
developing a product (Prophecy-TM-) in this area. It is envisioned
that, subject to mutual agreement, Progenitor will be actively involved
in specification of such product and, if so, will be offered the
opportunity to participate as a beta test site for planned releases of
the
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generally commercially available versions of this software product no
later than other beta test site customers and will offered the
opportunity to license such versions as soon as they become generally
commercially available.
Progenitor has, or is planning to have, certain technologies and
capabilities that may be useful for validating the results of Pangea's
protein structure and function prediction tools. Additionally,
Progenitor has, or is planning to have, certain technologies and
capabilities that may be useful for validation and verification of
biological information arising from other Pangea products. If Pangea
desires access to such technologies and capabilities for the purpose of
validating the results of its tools or for validation and verification
of such biological information, then, subject to mutual agreement,
Progenitor will assign appropriate personnel and other resources to
accomplish this project and Pangea will provide funding for the effort
in an amount equal to Progenitor's access (or negotiated royalty rights
in lieu of such funding).
- Research in the area of human genetics, and development of new tools for
analysis of data related to human genetics. Pangea is planning to add
such functionalities to its product suite. If Progenitor desires this
additional functionality to be available more quickly than scheduled by
Pangea, then, subject to mutual agreement, the scope of an appropriate
acceleration project will be mutually agreed to, Pangea will assign
software engineers to accomplish this project and Progenitor will
provide funding for the project on mutually agreed terms.
- Developing gene expression analysis tools (ExpressionCity-TM-), a
consensus database (GeneForest-TM-) and utilizing polymorphism and
mutation data and high throughput screening data. This may be another
area for collaborative effort between the two companies.
Pangea would like to make use of Progenitor's polymorphism and mutation
data surrounding given disease states for use in a federated database of
diagnostic disease or clinical trial information. Pangea would also
like to make use of any high-throughput screening data, including data
related to failures, that Progenitor could make available. Utilization
of such data represents other areas for potential collaboration between
the two companies.
Therefore the parties agree upon the following:
I. Progenitor has licensed off-the-shelf versions of GeneWorld-TM- and
Pangeanetics-TM-. Pangea will endeavor to add enhancements to these
products requested by Progenitor, and agreed upon by Xxxxxx, as part of
Pangea's support and maintenance efforts. If there are additions that
require significant effort beyond the scheduled upgrades, the parties
will discuss these individually and, subject to mutual agreement, agree
upon deliverables, funding and other terms.
II. Pangea will appoint Progenitor as a principal beta site for testing
planned releases of the generally commercially available versions of new
bioinformatics systems
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and technologies developed by Pangea and, as such, upon commercial
release of the software product for which Progenitor was serving as a
beta test site, Progenitor will be able to purchase licenses to use
the software at a discount of [***] of the license (or such other
amount as the parties agree). Progenitor agrees to act as a beta
customer for such products on reasonable and customary terms for beta
site arrangements.
III. In cases where Pangea develops generally commercially available
versions of products that are of no initial interest to Progenitor (at
the time of this agreement or during beta testing) Pangea will offer
to Progenitor the ability to purchase licenses to such generally
available products at a discount of [***] of the license (during the
first year of release of the product subject, to mutual agreement).
IV. In areas of collaboration where Pangea elects to fund a protein
structure and function validation project, or project for validation and
verification of biological information arising from other Pangea
products, subject to mutual agreement, Pangea will fund and
scientifically advise each such project. Progenitor will assign
appropriate personnel and other resources to accomplish this project and
Pangea will provide funding for the effort equal to Progenitor's costs
(or negotiated royalty rights in lieu of such funding).
V. In areas of collaboration where Progenitor elects to fund a project
under which Progenitor will be the primary source of funding for
development costs, subject to mutual agreement, Pangea will initiate
research to evaluate, recommend and, if possible, develop new tools.
Upon such election, Progenitor will fund (at the agreed upon rate) and
scientifically advise the required FTEs. Pangea, in return, will
license to Progenitor free of charge software developed under such
project and will use reasonable efforts to support and maintain the
software for a mutually agreed time period at a mutually agreed upon
price.
VI. [***]
VII. No right, title or interest in, to or under any intellectual property
owned or otherwise controlled by Progenitor or Pangea is granted or
implied. Any grant of any right or license in, to or under any
intellectual property owned or otherwise controlled by Progenitor or
Pangea shall be made only by a separate written agreement between the
parties.
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VIII. This document is being entered into in good faith between Progenitor and
Pangea. This document is not intended to bind the parties regarding
matters that are specified to be subject to mutual agreement between the
parties, unless and until such agreement is reached. For any matters
that are subject to later agreement of the parties, this document
constitutes an agreement to negotiate in good faith to reach, if
reasonably possible, agreement regarding such matters.
IX. Each Party shall bear its respective costs, fees and expenses in
connection with the collaborations contemplated by this document except
as otherwise agreed to by the parties hereto. This document shall not
create any form of joint ventures or partnership between the parties and
neither party shall take any contrary position nor shall either party be
entitled to, or for any reason attempt to, enter into any legal
obligation on behalf of the other. Neither party shall disclose the
terms or existence of this Agreement except to the extent mutually
agreed by Progenitor and Xxxxxx.
The terms of this document will be reviewed annually on the anniversary of this
agreement by the appropriate officers of Progenitor and Pangea. At each such
review, Progenitor and Pangea will determine whether the terms of this agreement
should be extended or changed. However, since this is an initial agreement, the
parties will develop a more detailed working document, as appropriate, in which
mutually agreed upon timelines, functionality and other appropriate terms will
be stated. In any event, unless Progenitor and Xxxxxx agree in writing to
extend the term of this document at the end of each one-year period, all rights
and obligations specified above, other than ownership of intellectual property
as specified in Paragraph VII, will terminate.
I agree that the terms set forth in this document are an accurate summary of the
understanding reached between Progenitor and Pangea.
Xxxxxx and accepted on behalf of Progenitor.
Signature: /s/ Xxxxxxx X. Xxxxxxxx
--------------------------------
Name: Xxxxxxx X. Xxxxxxxx
-------------------------------------
Title: Vice President Corporate Development
------------------------------------
Date: 3/13/97
-------------------------------------
I agree that the terms set forth in this document are an accurate summary of the
understanding reached between Progenitor and Pangea.
Xxxxxx and accepted on behalf of Pangea.
Signature: /s/ Xxxxxxx Xxxxx
--------------------------------
Name: Xxxxxxx Xxxxx
-------------------------------------
Title: President
------------------------------------
Date: 3/13/97
-------------------------------------
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PRODUCT INFORMATION
GENETHESAURUS-TM-
The amount of biological annotations and information in public databases is
staggering. EMBL, NCBL, DDBJ, and hosts of smaller academic institutions have
placed their information in the public domain. Most bioinformatics projects
rely on this information as a standard to which unknown sequences can be
compared. Unfortunately, this data is often in messy, incomplete, and in flat-
file format, which limits its usefulness and accessibility.
To address these problems, Pangea is developing a relational structure for
biological information known as GeneThesaurus-TM-. The first version is
designed to incorporate databases like GenBank, SwissProt, Enzyme Commission
(EC), and YPD in a relational structure that allows for easy and intuitive
querying of the database. Any field in GenBank will be searchable -- including
fuzzy word searches for keyword and title lines. The hierarchical
categorizations provided by GeneThesaurus-TM- will allow for complex MDD (multi-
dimensional database) queries and data mining. Researchers will be able to
analyze expression data based on functional grouping, nearest neighbors,
keywords, and gene family.
GeneThesaurus-TM- will provide users easy access the public data banks in a
relational format. Public data is pre-processed to add additional annotation,
linkages between data sources, and then stored in a relational format. The
program will serve as a flexible repository of private and corporate databases,
containing sequences, annotations, mapping, and experimental information.
GeneThesaurus-TM- is designed to handle future growth. Some of the information
stored and searchable in GeneThesaurus-TM- is currently contemplated to include:
- function family / classification - cell / tissue /source localization
- functional Pathway mapping - gene name
- gene family - author /publication
- homology - keyword / synonym
- sequence features - disease relevance
- regulation (transcription and - patent information
expression)
- motif searching - database sub-selection
- chromosomal mapping
Future versions [may] include Medline, PDB, EMBL, Flybase, OMIM, Menagerie-TM-,
and GDB, subject to availability.
Menagerie-TM-, a compendium of model organism information will allow storing of
information about genes and protein for specific model organisms. Having access
to the
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vast amount of annotation information, available both publicly and privately,
will facilitate research on cross species comparisons, as well as contributing
more density and depth to the annotations available about any single gene and
protein.
EXPRESSIONCITY-TM-
ExpressionCity-TM- is Pangea's environment for sophisticated statistical
analysis and 3D data visualization of gene expression data. This data can be
derived from a variety of sources such as ESTs, hybridizations of arrays of
oligonucleotides, cDNA clones, and rapid analysis of small restriction
fragments. These data sources can be of both normalized, enriched and raw
libraries of transcripts.
ExpressionCity-TM- gives the user multiple perspectives on their data --
providing, for example, molecular classifications (within GeneThesaurus-TM-) and
biological sample pathology information.
GENEFOREST-TM-
GeneForest-TM- (Fast Overlapping of Redundant Expressed Sequence Tags) uses
high-powered algorithms and computing power to cluster smaller DNA fragments
into groups. This enables calculation of the intensity of gene expression as
well as generation of unique, full-length, consensus databases. GeneForest-TM-
plugs into GeneWorld-TM- for the purposes of sequence clean-up, identification
and discovery through "strategies". Sophisticated quality control processes
within GeneForest-TM- identify false and improper clusters.
PROPHECY-TM-
Prophecy-TM- is a package of advanced tools and database support for prediction
of protein structure and function. Protein sequences that have no match to a
known 3D protein structure or functional family by classical sequence alignment
methods can be further analyzed using a triad of more algorithms:
- Hidden Markov Models
- Alignment Threading with Optimized Scores
- Test of Optimal Mutagenesis
Users can store their own experimental or theoretical structural coordinates as
well as their own sets of sequences and multiple sequence alignments. Using
these tools, Pangea will attempt to predict and store the 3D structures for all
of GenBank in a relational format (Virtual PDB) within GeneThesaurus-TM-. This
will provide users early access to a model structure and hence enable them to
study function and activity more quickly. Virtual PDB will also allow
assessment of the predictive power of the tools and can be used as a benchmark
comparison with known structure solved by crystallography.
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