Open Source Model in Bioinformatics: Intellectual Property Challenges and Implications

Open Source Model in Bioinformatics:Intellectual
Property Challenges and Implications
Presentation made in the National Seminar on Intellectual Property Law

organised by HRD Ministry Govt. of India and AMU Law Faculty.
Dr. Tabrez Ahmad

Associate Professor of Law
www.site.technolexindia.com
tabrezahmad7@gmail.com
http://technolexindia.blogspot.com
Dr. Tabrez Ahmad,

7th February , 2010 Blog: http://iplexindia.blogspot.com, www 1
Dr. Tabrez Ahmad,
Agenda
1. What is Bioinformatics?
2. Intellectual Property In Bioinformatics
3. Concept Of Open Source Model
4. Application Of Open Source In Bioinformatics
5. Imbalane of Intellectual Property and Private
Public Debate
6. Open source Indian Scenario
7. Economic Aspects of Open Bioinformatics and
Future Course of Action
Dr. Tabrez Ahmad,

7th February , 2010 Blog: http://iplexindia.blogspot.com,
3 www
Digital Revolution Internet Infra in INDIA
Internet
INDIA Internet
Infrastructure:2008.5 1Mil. Domains
(0.5 Mil. “.in”)
Bharti
BSNL NIC
130+ IDCs 134 Major Mail Servers

ISPs
ERNET
Reliance
TATA
Communications
4.8 Mil. High DNS

Speed Internet
Enterprise
IT /
65 Mil. Internet Govt. ITES
Users BPO
Home
248 Mil. Mobile Academia
Phones
8 Mil. Mobile Phones being added
per month
`
Tele Density 24 per 1000 person

Targetted Broadband connection = 10 Mil. VOIP, IPTV
(2010) Dr. Tabrez Ahmad, 4
What is Bioinformatics
 Bioinformatics is the use of
computational tools and databases
in relation to genomic
and proteomic medical
and health data.
Dr. Tabrez Ahmad,

Bioinformatics is the collective name
for the application of information
technology to fields such as Molecular
Biology, Biotechnology, Medicine and
Agriculture.
The products of bioinformatics

include:
collections of protein sequences, as well
as analytical computer software.
Dr. Tabrez Ahmad,

Bioinformatics currently deals with several
main types of biological data
Sequences and structure of genes;
-3--D molecular structures; Genome
structures and functions;
Dr. Tabrez Ahmad,

Bioinformatics incorporates
algorithms for the analysis of DNA
sequences,
protein sequences,
determinations of the interactions between
biological macromolecules such as
proteins
determinations of networks of interacting
molecules in a biological cell.
Discovering gene expression patterns
requires computational power.
Dr. Tabrez Ahmad,
The majority of bioinformatics
inventions involve applications of :
computer-implemented protocols or
software in
 collecting,
storing,
processing, or
analyzing biological data.
Dr. Tabrez Ahmad,

IP Protection in Bioinformatics
Obtaining intellectual property protection for
bioinformatics and related technology is a
vitally important process. As it not only
afford the owner, the right to exclude
others from using the protected
technology, but can also potentially provide
the owner a monopoly position for the
manufacture and sale of the technology.
Dr. Tabrez Ahmad,
1. Patents : Through patents,
companies and entrepreneurs can
obtain a legal monopoly to protect
their technology from being
manufactured and sold by
competitors,thus making patents
an important incentive for
technology development and
innovation.
Dr. Tabrez Ahmad,
In the U.S. Patent and Trademark
Office; three types of patents exist: utility,
plant and design. Of these, the utility
patentis the type most commonly
associated with Bioinformatics
Inventions and can be obtained for a
new, useful and non-obvious process,
machine, manufacture or composition of
matter, or a new and useful improvement
of any of the aforementioned.
Dr. Tabrez Ahmad,
Claimable Aspects of Bioinformatics
Patents can be obtained for such bioinformatics areas
as:
the computational and analytical aspects of
genomics and proteomics which includes
algorithms, sequence analysis techniques,
mapping techniques, comparison techniques,
primer design, phylogenetic analysis,
molecular modeling, protein structure prediction
and protein function prediction), databases (for
example, construction, querying and data mining),
biological integrated circuits, micro arrays, and
image analysis.
Dr. Tabrez Ahmad,
Types of Bioinformatics Patents
 Bioinformatics database structures (US Pat
No. 6,023,659 (2000)).
Computer based methods of determining the
actions of drug candidates on cellular targets
(US Pat No. 6,300,078 (2001)).
Methods for modeling molecular interactions
for rational drug design (US Pat No.
5,787,279 (1998)).
Use of 3--D protein structures in rational drug
design (US Pat No. 6,225,076 (2001)).
Dr. Tabrez Ahmad,
Bioprospecting and the new IPR regime
Given the global trends in capturing the

intellectual property markets, the Third World
nations like India needs to look ahead for the best
possible ways and means by which they can
generate IPR and build up IPR covered
bioindustrial regimes.
Biotechnology (BT), Information Technology
(IT) and Herbal Technology (HT) are the three fast
emerging and powerful areas of R&D in current
century. The rich biodiversity, associated
knowledge systems and human resources etc. are
the strength of Asia-pacific countries, and therefore
have the best opportunity.
Dr. Tabrez Ahmad,
Bioprospecting
Chemical Prospecting Gene Prospecting

Drugs and pharmaceuticals
Genetic engineering
Pesticides
Crop development
Cosmetics
Fermentation
Food additives
Cell culture
Other industrially valuable
Chemical products
Bionic Prospecting
Designs
Sensor technologies
Architecture
Bioengineering
Biomodeling
Dr. Tabrez Ahmad,
Bioprospecting: Linkages and leads
Biodiversity Biotechnology Bioprospecting

& IK/TK
Information
technology
Drug development
Herbal Pharmaceuticals
technology
Agrochemistry
Cosmetics
Proteins
Conservation Sustainable Benefit Bioinformatics Enzymes
use sharing New crop varieties
GMOs
GM foods
Designs etc.
IPR
Dr. Tabrez Ahmad,
2. Trade Secrets. It can be used to
protect Bioinformatics-related
Intellectual Property such as software
code, manuals,:
compilations of facts
(databases),formulas and processes.
Dr. Tabrez Ahmad,

3. Copyrights: Copyright can be used
to protect bioinformatics-related
materials such as scientific articles,
books, software code, manuals, Web
pages, graphic artwork, multi-media
works, compilations of facts
(databases).
Dr. Tabrez Ahmad,
4 .Licensing: : The time, effort and
cost associated with acquiring and
protecting intellectual property
assets may be recovered, at least
to some degree, through licensing.
5. Trademarks: Trademarks can be
used to protect trade names,
product names, domain names, and
service marks/slogans for
bioinformatics companies.
Dr. Tabrez Ahmad,
Open Source and Intellectual Property
Dr. Tabrez Ahmad,

Open Source
What is it?
Non-proprietary software development
Code is modified cooperatively by a
community of users
Copyright law is applied to restrict the
restriction of use of the code in order to
ensure that any and all users can
access and modify the source code for
their own purposes
Dr. Tabrez Ahmad,

Hallmarks of the process
Parallel as opposed to linear
development of software
functionality
Continuous as opposed to staged -
testing
Examples
Sendmail
Apache web server
Perl scripting language
Linux OS
Dr. Tabrez Ahmad,
Open Source
Recent history
1960-80
Focus on academic computer science at
places like Berkeley, MIT, CMU, as well as
corporate research facilities like Bell Labs
and Xerox’s Palo Alto Research Center
Unix, C (Bell Labs)
Simultaneous development of networks
Usenet and later Arpanet
Dr. Tabrez Ahmad,

The Open Source Alternative
 Open Source Software (OSS):
 OSS defined: Software obtainable for no more than the
reasonable cost of reproduction in which source code is
freely distributed with the right to modify the code, on the
condition that redistribution is not restricted.
 Not the same as public domain – author usually retains
copyright in work and only grants licenses under non-
traditional terms and conditions.
Dr. Tabrez Ahmad,

Blog:
http://iplexindia.blogspot.com,
www
7th February , 2010 25
The Open Source Alternative (cont.)
OSS is increasingly mainstream.
 IBM and other large companies are
investing billions in OSS.
 The majority of web servers on the
Internet use the OSS program Apache.
Dr. Tabrez Ahmad,

Blog:
www
1980-90
In the early ‘80’s, AT&T began to treat Unix
as proprietary, at which point different
“flavors” of the OS emerged (Berkeley’s BSD
Unix, HPUX, Sun)
Emergence of formal rules in response to
AT&T’s threats of litigation to govern open

source development
Free Software Foundation (R. Stallman,
MIT) 1983 in USA and 2001 in India.

GNU software and the General Public
License (GPL)
Dr. Tabrez Ahmad,
Open Source
 Open source licensing terms:
 No licensing restrictions imposed on others’ use of code
 All code, whether developed cooperatively or separately,
licensed on the same terms
 Not use copyright law to restrict downstream
“enclosure” (i.e. proprietarization) of code. This is the
distinction between open source and public domain
software.
 Evolution of open source organizational structures
 Distinction between contributing programmers and
leadership group having control over changes in the
“official” version of the software
Dr. Tabrez Ahmad,
Open source
1990-Present
Widespread diffusion of internet
Introduction of Linux OS
“Debian Social Contract”
Movement away from the “viral” nature of the
GPL to allow use of open source code in
proprietary software without requiring that the
larger packet be released as open source.
Dr. Tabrez Ahmad,

Challenges of managing open source
Forking and splintering: development
of competing variations
Market segmentation in favor of high-
end users at expense of low-end:
support, documentation, user-
interface
Dr. Tabrez Ahmad,
Open source
Economic Theory and Open Source
Altruism?
Other motivations: immediate versus delayed costs
and benefits
Immediate benefits
Direct compensation if employer encourages open
source activities
Benefit in use if work involves fixing a bug or
improving software the programmer uses regularly

Immediate costs
Opportunity cost of time spent on open source
project
Dr. Tabrez Ahmad,
Open source
Delayed rewards: Signaling incentives
Career concerns
Ego gratification
Signaling dimensions
Visibility of performance to relevant audiences
(peers, labor market, venture capital community)
Effort impact on performance
Information content of performance about talent
Dr. Tabrez Ahmad,

Open source
Open Source versus Commercial Incentives
Commercial
Proprietary control of code allows it to generate
income, which can be used to compensate
programmers.
Greater control in allocation of specific
resources
Costs associated with the need for secrecy in
development of code and for copy protection
efforts
Dr. Tabrez Ahmad,

Open Source
Reduced revenues when code is given away
Reduced costs associated with
“Alumni effect”: Freely available code gets
incorporated in teaching activities, which
leads new generations to adopt the same
software, reducing downstream training
costs. (Unix)
Customization and bug-fixing: Direct external
benefit associated with parallel development
and innovation
Transparency of process and functionality
Full initiative
Minimal lock-in
Dr. Tabrez Ahmad,

Open source
Leadership, Organization and Governance
Issues
Large open source projects need
leadership and rules to avoid splintering
Leadership activities
Provide a vision of the end result(s) of the
project
Assemble a critical mass of initial code to
demonstrate value of the project and

promise for the future
Dr. Tabrez Ahmad,
Organize production modules
Components must be doable and
contribute to the overall project

Attract programmers to the project
Ensure that component modules provide
sufficient challenge
Hold project together
Be able to make hard-nosed decisions
about which components end up being part

of the “official” version of the software
Dr. Tabrez Ahmad,

Open source
Governance
Single strong
leader (Torvalds with Linux)
Governance committee
Issues of trust, ability to communicate, willingness
to compromise in the face of merit, clarity in

evaluation procedures
Open Source and Commercial Software Development
Commercial duplication of open source incentives?
Some efforts by major players to adopt open source
processes
Microsoft, HP
Netscape’s Mozilla project

Dr. Tabrez Ahmad,
Open source
Commercial strategies
 Provision of complementary products and services
 Documentation
 Installation and configuration wizards

 Support
 Provision of expertise in support of open source projects

 Intermediation between corporate clients and open
source community
 Certification
 Conduit to venture capital community

 Example: Collab.Net
Dr. Tabrez Ahmad,

Open source
Open questions about open source
Does the modularization required for effective
management of open source development
scale?
Report of the President’s Information
Technology Advisory Committee indicates
some belief by experts that it does
Does open source management activity scale?
How durable are open source products?
Dr. Tabrez Ahmad,

What are open standards?
Not just “open mouth”. Merged
Perens'/Krechmer's/EC's definition:
1. Availability: available for all to read and implement
2. Maximize End-User Choice: Create a fair, competitive
market for implementations; NOT lock the customer
in. Multiple implementors
3. No Royalty: Free for all to implement, with no royalty
or fee
4. No Discrimination: Don't favor one implementor
over another (open meeting, consensus/no
domination, due process)
Dr. Tabrez Ahmad,
5. Extension or Subset: May be extended or offered
in subset form
6. Predatory Practices: May employ license terms
that protect against subversion of the standard by
embrace-and-extend tactics
7. One World: Same standard for the same
capability, world-wide
8. On-going Support: Supported until user interest
ceases
9. No or nominal cost for specification (at least;
open access?)
Dr. Tabrez Ahmad,

Most popular OSS
licenses
Many licenses, but most use Top Ten OSS Licenses
GPL, and over 3/4 projects GPL: 65.50%
use top 10 LGPL: 6.53%
"Do not write a new license
BSD-old: 2.93%
if it is possible to use [an
existing common license]... BSD-new: 2.86%
many different and MIT: 1.67%
incompatible licenses works Artistic: 1.55%
to the detriment of OSS Public Domain: 1.15%
because fragments of one
program can not be used in Apache 2.0: 0.86%
another program with an MPL: 0.72%
incompatible license.” - Apache (orig.): 0.56%
Bruce Perens Dr. Tabrez Ahmad, [Freshmeat 2007-07-31]
Advantages and Disadvantages of Open
Source Software
Advantages:
 No direct cost to user.
Zero marginal cost of scale because open source

doesn't require additional licenses as installation
grows.
 Freedom and flexibility to modify the software.
 Portable to a wide range of platforms giving user wider
choice of hardware.
 Avoidance of proprietary lock-in: OSS not dependent on
subsequent purchase of related vendor products or
updates.
Dr. Tabrez Ahmad,
Blog:
www
Advantages and Disadvantages of Open
Source Software
Disadvantages:
 Legal challenges possible: Due diligence is required to
verify that original distributor had right to distribute
source code under the IP laws.
 General Public License (GPL) often included: Any
modifications or additions to GPL-licensed software must
also be licensed under the same terms.
 Concerns that support may be difficult to obtain.
 Cost savings may be outweighed by training and
customization costs.
Dr. Tabrez Ahmad,

Blog:
www
Recent Government Initiatives Toward
Open Source Software in USA
 Massachusetts – All agencies documents must be created
and saved in open source programs.
 U.S. Office of Management and Budget – On July 1, 2004,
OMB officially recognized OSS as a viable option for civilian
agencies of the federal government.
 Government Open Code Collaborative: a voluntary
collaboration between public sector entities and non-profit
academic institutions created for the purpose of
encouraging the sharing, at no cost, of computer code
developed for and by government entities where the
redistribution of this code is allowed. http://www.gocc.gov/
Dr. Tabrez Ahmad,

Blog:
www
Interpreting Open Source Licenses
Needs Expert Interpretation and fit with business
Example: Sun Binary Code Distribution License
Agreement
7 page document
Sun grants you a … license …[to] distribute the Software,
provided that … and (vi) you agree to defend and indemnify
Sun and its licensors from and against any damages, costs,
liabilities, settlement amounts and/or expenses (including
attorneys' fees) incurred in connection with any claim,
lawsuit or action by any third party that arises or results
from the use or distribution of any and all Programs and/or
Software
Dr. Tabrez Ahmad,
© Copyright 2009 Protecode Inc. Proprietary 46
Application of Open Source in
Bioinformatics
Dr. Tabrez Ahmad,

Public &
Private Domain
While the product,
design, or process is
protected, it remains in
the Private Domain,
SHAPE NAME thereby granting the
+ holder of the Patent a
functional monopoly.
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
+ Then the patent expires.
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
SHAPE NAME
MANUFACTURE
Dr. Tabrez Ahmad,

Public &
Private Domain
Unless the name,

method of manufacture
or design are severable,
SHAPE NAME (e.g. Sunbeam)
+ all elements of a
product transition to the
MANUFACTURE
public domain upon
expiration of the patent.
Dr. Tabrez Ahmad,

The Open Bioinformatics Foundation
supports projects similar
to Bioconductor that are nominally rooted
in specific programming languages.
 BioPerl ,
 BioPython and
BioJava are prominent examples of open-
source language-based bioinformatics
projects.
Dr. Tabrez Ahmad,

Open Source Indian Scenario
Though the IT Sector ins booming in India, the
concept of Open Source is not commonly known.
Therefore, there is neither any specific Indian
policy on OSS, nor is there a specific legislation
framed by the Indian Legislature on this, however
endeavors are being made to rectify the situation
For instance Prof. Deepak B Pathak at IIT
Mumbai has begun an effort to create an Open
Source License, ie,
Knowledge Public License ( KPL)
Dr. Tabrez Ahmad,

Economic aspects of open Bioinformatics
and Future Course of Action
Solution of economic recession is possible
by free sharing of IP loc-kin technologies
Obama was criticized and opposed by US
multinationals for promising to remove IP
cap from green technologies and give free
license to developing countries.
So in the present scenario open
bioinformatics is the viable solution for
hassle free sharing of the technology
Dr. Tabrez Ahmad,
Do you have any question?
Dr. Tabrez Ahmad,

Thanks
Dr. Tabrez Ahmad,


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Open Source Model in Bioinformatics:Intellectual

Property Challenges and Implications

Presentation made in the National Seminar on Intellectual Property Law

Dr. Tabrez Ahmad

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

130+ IDCs 134 Major Mail Servers

4.8 Mil. High DNS

Tele Density 24 per 1000 person

Dr. Tabrez Ahmad,

The products of bioinformatics

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Given the global trends in capturing the

Chemical Prospecting Gene Prospecting

Biodiversity Biotechnology Bioprospecting

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Internet use the OSS program Apache.

Dr. Tabrez Ahmad,

AT&T’s threats of litigation to govern open

MIT) 1983 in USA and 2001 in India.

Dr. Tabrez Ahmad,

improving software the programmer uses regularly

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

demonstrate value of the project and

contribute to the overall project

about which components end up being part

Dr. Tabrez Ahmad,

Issues of trust, ability to communicate, willingness

to compromise in the face of merit, clarity in

Netscape’s Mozilla project

 Installation and configuration wizards

 Provision of expertise in support of open source projects

 Conduit to venture capital community

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

+ Then the patent expires.

Dr. Tabrez Ahmad,

Unless the name,

Dr. Tabrez Ahmad,

Dr. Tabrez Ahmad,