INFORMATICS LECTURE MIDTERMS

I. OPEN SOURCE SOFTWARE/ FREE SOFTWARE

Background
 The key commonality between FSF and OSI philosophies is that the source
code is made available to the users by the programmer.
 Where FSF and OSI differ in the restrictions placed on redistributed source
code. FSF is committed to no restrictions, so that if you modify and
redistribute free software, as a part or as a whole of aggregated software, you
are not allowed to place any restrictions on the openness of the resultant
source code (Wong & Sayo, 2004). The difference between the two
movements is said to be that the free software movement’s fundamental
issues are ethical and philosophical, while for the open source movement the
issues are more practical than ethical ones; thus, the FSF asserts that open
source is a development methodology, while free software is a social
movement (FSF, 2010a).

 Proprietary software is that on which an individual or company holds the

exclusive copyright, at the same time restricting other people’s access to
the software’s source code and/or the right to copy
 Commercial software is software developed by businesses or individuals
with the aim of making money from its licensing and use.
 Freeware is software offered free of charge, but without the freedom to
modify the source code and redistribute the changes, so it is not free
software (as defined by the FSF).
 Shareware is another form of commercial software, which is offered on a
“try before you buy” basis. If the customer continues to use the product
after a short trial period, or wishes to use additional features, they are
required to pay a specified, usually nominal, license fee.
 A. Free Software - The license shall not restrict any party from selling or giving
 defined by the FSF in terms of four freedoms for software users: to away the software as a component of an aggregate software
have the freedom to use, study, redistribute, and improve the distribution containing programs from several different sources.
software in any way they wish. - The license shall not require a royalty or other fee for such
 Free software is described in terms of the users’ freedom to run, sale.
copy, distribute, study, change, and improve the software. Rationale: By constraining the license to require free redistribution, we eliminate the
 More precisely, it refers to four kinds of freedom for the users of the temptation to throw away many long-term gains in order to make a few short-
software: term sales dollars. If we did not do this, there would be lots of pressure for
a. Freedom 0- The freedom to run the program for any purpose cooperators to defect.
b. Freedom 1- The freedom to study how the program works, 2. Source Code – cannot be reversed
and change it to make it do what you wish. Access to the source - The program must include source code, and must allow
code is a precondition for this. distribution in source code as well as compiled form.
c. Freedom 2- The freedom to redistribute copies so you can help - Where some form of a product is not distributed with source
your neighbor. code, there must be a well-publicized means of obtaining the
d. Freedom 3- The freedom to distribute copies of your modified source code for no more than a reasonable reproduction cost
versions to others. By doing this you can give the whole preferably, downloading via the Internet without charge.
Community a chance to benefit from your changes. Access to the - The source code must be the preferred form in which a
source code is a precondition for this. programmer would modify the program. Deliberately
obfuscated source code is not allowed.
Note: - Intermediate forms such as the output of a preprocessor
If there is a mistake or inappropriate code, the programmers will update the original or translator are not allowed.
source code (derived/ old version) + the new source code = new version Rationale: We require access to unobfuscated source code because you cannot
evolve programs without modifying them.
If illegal, programmers will update then delete previous updates 3. Derived Works – original software, past or previous
- The license must allow modifications and derived works, and
B. Open Source Software must allow them to be distributed under the same terms as the
 said to promote software reliability and quality by supporting license of the original software.
independent peer review and rapid evolution of source code as well as Rationale: The mere ability to read source is not enough to support
making the source code of software freely available. independent peer review and rapid evolutionary selection.
 In addition to providing free access to the programmer’s instructions to 4. Integrity of the Author’s Source Code
the computer in the programming language in which they were written, many - The license may restrict source code from being distributed in
versions of open-source licenses allow anyone to modify and redistribute the modified form only if the license allows the distribution of
software. “patch files” with the source code for the purpose of modifying
 The open-source initiative (OSI) has created a certification mark, “OSI the program at build time.
certified.” In order to be OSI certified, the software must be distributed under Rationale: Encouraging lots of improvement is a good thing, but users have a right
a license that guarantees the right to read, redistribute, modify, and use the to know who is responsible for the software they are using. Authors and
software freely maintainers have reciprocal right to know what they are being asked to support and
 Not only must the source code be accessible to all, but also the distribution protect their reputations.
terms must comply with 10 criteria defined by the OSI. 5. No Discrimination Against Persons or Groups – for everybody
 The distribution terms of open-source software must comply with the following - The license must not discriminate against any person or
criteria: group of persons.
1. Free Redistribution
Rationale: In order to get the maximum benefit from the process, the maximum Rationale: This provision is aimed specifically at licenses which require an explicit
diversity of persons and groups should be equally eligible to contribute to open gesture of assent in order to establish a contract between licensor and licensee.
sources. Therefore, we forbid any open source license from locking anybody out of Provisions mandating so-called “click-wrap” may conflict with important methods of
the process. software distribution such as FTP download, CD-ROM anthologies, and Web
6. No Discrimination Against Fields of Endeavor mirroring; such provisions may also hinder code reuse.
- The license must not restrict anyone from making use of
the program in a specific field of endeavor. For example, it II. OSS/FS Development Models and Systems
may not restrict the program from being used in a business, or Bazaar method of development
from being used for genetic research.  OSS/FS development is likened to a bazaar, growing organically from an
Rationale: The major intention of this clause is to prohibit license traps that initial small group of traders or enthusiasts establishing their structures
prevent open source from being used commercially. and beginning businesses.
7. Distribution of License  The bazaar grows in a seemingly chaotic fashion, from a minimally
- The rights attached to the program must apply to all to whom functional structure, with later additions or modifications as
the program is redistributed without the need for execution circumstances dictate.
of an additional license by those parties.  Likewise, most OSS/FS development starts off highly unstructured,
- No need to ask original publisher with developers releasing early, minimally functional code and then
Rationale: This clause is intended to forbid closing up software by indirect modifying their programs based on feedback. Other developers may
means such as requiring a nondisclosure agreement. then join, and modify or build on the existing code; over time, an entire
8. License Must Not Be Specific to a Product operating system and suite of applications develops, evolves, and
- The rights attached to the program must not depend on the improves continuously.
program’s being part of a particular software distribution. If the  The bazaar method of development is said to have been proven over time to
program is extracted from that distribution and used or have several advantages, including the following:
distributed within the terms of the program’s license, all a. Reduced duplication of efforts through being able to examine the
parties to whom the program is redistributed should have work of others and through the potential for large numbers of
the same rights as those that are granted in conjunction contributors to use their skills.
with the original software distribution. b. Building on the work of others, often by the use of open standards
Rationale: This clause forecloses yet another class of license traps. or components from other applications
9. License Must Not Restrict Other Software c. Better quality control; with many developers working on a project,
- The license must not place restrictions on other software code errors (bugs) are uncovered quickly and may be fixed even more
that is distributed along with the licensed software. For rapidly (often termed Linus’ Law, “given enough eyeballs, all bugs are
example, the license must not insist that all other programs shallow” [Raymond, 2001])
distributed on the same medium must be open source d. Reduction in maintenance costs; costs, as well as effort, can be
software. shared among potentially thousands of developers (Wong & Sayo,
- McCafé + Casper in one installation 2004).
Rationale: Distributors of open source software have the right to make their
own choices about their own software. III. Proposed Benefits of OSS/FS
10. License Must Be Technology-Neutral 1. Can transform healthcare
- No provision of the license may be predicated on any  OSS/FS has been described as the electronic equivalent of generic drugs
individual technology or style of interface.  In the same way as the formulas for generic drugs are made public, so
- No demands of external or internal storage or minimum/ OSS/FS source code is accessible to the user.
maximum capacity  Any person can see how the software works and can make changes to
the functionality. It is also suggested by many that there are significant
 similarities between the open source ethos and the traditional scientific assisted living communities, clinics [public health and educational venue
method approach clinics], and home care).
 As OSS/FS can be obtained royalty free, it is less expensive to acquire  OSS/FS has been very successful in other information-intensive industries, and
than proprietary alternatives. This means that OSS/FS can transform so is seen as having potential to integrate functional EHR systems into, and
healthcare in developing countries just as the availability of generic drugs across, wider health systems. They believe that interoperable open source
have. EHR systems would have the potential to improve healthcare in the
2. Lack of the proprietary lock-in that can often freeze out innovation, and with United States, and cite examples from other areas around the world.
OSS/FS projects supporting open standards  Examples exist of OSS/FS electronic medical records (EMRs), hospital
3. Providing a level playing field, expanding the market by giving software management systems, laboratory information systems, radiology
consumers greater choice (Dravis, 2003). information systems, telemedicine systems, picture archiving and
4. Security, reliability, and stability, and developing local software capacity. communications systems, and practice management systems.
Many of these proposed benefits have yet to be demonstrated or tested  A few examples indicate this range, and more extensive lists and
extensively descriptions are available at several Web portals, including www.
medfloss.org.
III. OSS/FS HEALTHCARE APPLICATIONS
 It is suggested that in healthcare, as in many other areas, the development of ClearHealth (www.clear-health.com)
OSS/FS may provide much-needed competition to the relatively closed  ClearHealth is a Web-based, fully comprehensive medical suite offering a
market of commercial, proprietary software, and thus encourage wide range of tools to practices of all sizes.
innovation.  It includes scheduling and registration features; EMR including alerts,
 This could lead to lower cost and higher quality systems that are more patient dashboard, laboratory ordering and results, and barcode
responsive to changing clinical needs. generation and uses; SNOMED; access via mobile devices; billing and
 OSS/FS could also solve many of the problems health information reporting features; and specialist clinical modules
systems (HISs) currently face including lack of interoperability and
vendor lock-in, cost, difficulty of record, and system maintenance given Indivo (indivohealth.org)
the rate of change and size of the information needs of the health
 Indivo is the original personal health platform, enabling an individual to
domain, and lack of support for security, privacy, and consent. This is
own and manage a complete, secure, digital copy of her health and
because OSS/FS more closely conforms to standards and its source code
wellness information.
open to inspection and adaptation.
 Indivo integrates health information across sites of care and over time.
 Bowen et al. (2009) summarize a number of advantages that open source
 Indivo is free and open source, uses open, unencumbered standards,
software offers when compared with proprietary software, including, but not
including those from the SMART Platforms project and is actively
limited to, the following:
deployed in diverse settings.
1. ease of modification and or customization,
 Indivo is an OSS/FS personally controlled health record (PCHR) system,
2. large developer community and its benefits, using open standards.
3. increased compliance with open standards,  A PCHR enables individuals to own and manage a complete, secure,
4. enhanced security, digital copy of their health and wellness information.
5. increased likelihood of source code availability in the event of the
demise of the vendor or company, SMART Platforms Project (smartplatforms.org)
6. easier to adapt for use by healthcare students, and  The SMART Platforms project is an open source, developer- friendly
7. flexibility of source code to adapt to research efforts. application programming interface and its extensible medical data
representation and standards based clinical vocabularies.
 The cost-effectiveness of open source software also lends well to communities
or organizations requiring such an approach (e.g., long-term care facilities,
  SMART allows healthcare clients to make their own customizations, and  raw uninterrupted facts that are without meaning
these apps can then be licensed to run across the installed base. ex. A patient’s weight is recorded as 168 lb, without additional
information this fact or datum cannot be interpreted
GNUMed (gnumed.de)  when data is interpreted information is produced
 The GNUmed project builds free, liberated open source EMR software in  for data to be interpreted and information produced, the data must
multiple languages to assist and improve longitudinal care be processed.
 It is made available at no charge and is capable of running on GNU/  DATA – INFORMATION – KNOWLEDGE
Linux, Windows, and Mac OS X. It is developed by a handful of medical  Several approaches to organizing data: sorting, classifying,
doctors and programmers from all over the world. summarizing, and calculating.

OpenMRS (openmrs.org) – outdated, for HIV patients Database

 OpenMRS® is a community-developed, open source enterprise EMR  Organized collection of related data
system platform (Wolfe et al., 2006).
 Placing notes in folders and folders in cabinets is one example of
 Of particular interest to this project is supporting efforts to actively build
creating a database
and/or manage health systems in the developing world to address AIDS,
 Can be stored and organized in many different formats
tuberculosis, and malaria, which afflict the lives of millions.
Ex. Phonebook, patient’s medical record
District Health Information System (sourceforge.net/projects/dhis/)
Types of data
 The District Health Information System (DHIS) provides for data entry,
1. Computer-based data
report generation, and analysis.
 It is part of a larger initiative for healthcare data in developing countries,  Alphanumeric data include letters and numbers in any combination
called the Health Information System Programme (HISP).  The numbers in an alphanumeric field cannot perform numeric
function
 Ex. Of alphanumeric data: social security number
OpenEHR (www.openehr.org)
 Numeric data are used to perform numeric functions including
 The openEHR Foundation is an international, not-for profit organization
adding, subtracting, multiplying, and dividing.
working toward the development of interoperable, lifelong EHRs.
 However, it is also looking to re-conceptualize the problems of health records,  Logic data are limited to two options: YES, or NO, TRUE or
not in narrow IT-implementation terms, but through an understanding of the FALSE, 1 or 2, ON or OFF.
social, clinical, and technical challenges of electronic records for healthcare in
the information society. - Cloud Server
 The open EHR Foundation was created to enable the development of open o Server
specifications, software, and knowledge resources for HISs, in particular EHR o Mobile
systems. o Notebook
o Database
Tolven (www.tolvenhealth.com)
o Network
 developing a range of electronic personal and clinician health record
applications, using open source software and health industry standards,
2. Conceptual Data Types – how did you use the data on your study?
including Unified Medical Language Systems and Health Level 7.
 Reflect how users view the data
 Can be based on the source of data
Data processing
 Ex. Lab produces lab data, X-ray department produces image data
Data
  Can also be based on the event that the data are attempting to  There are three basic types of data processing operations: data input, data
capture processing, and data output

Types of files Input

1. Data Files Data processing Output
processes processes
 Contain data that have been captured and stored on a computer Enter data processes
Inquire
using a software program Update data Store data
Retrieve
 Ex. Microsoft word document- will have the extension DOC. Chanage or Sort Report
modify data Transform
2. Processing Files Classify
 Executable files consist of a computer program or set of instructions Compare
that, when executed, causes the computer to open or start a specific
computer program or function. Summarize
 Files that tell a computer what actions the computer should perform Aggregate
when running a program.
 Ex. gmg. The Nursing Context

Fields, Records, and Files

 Each of the blocks or cells in the table is a field
 The top row lists the field names
 Field attribute- specific datum for that field for that record.
 Each row represents a record
 Each row is assigned a primary identifier
 A primary identifier is unique to that record.
 All the records in the table constitute a file
ID F- L-NAME ADDRESS ADDRESS- CITY REGION
NAME -1 2
0 Betty Santos Gen. Luna Bonifacio Baguio CAR
1 Rd. Street City
0 Leslie Magtibay Marcos Kennon Tuba CAR
2 Highway Road

Common Database Operations

 DBMS vary from small programs running on a personal computer to massive
programs that manage the data for large international enterprises.
 No matter what size or how a DBMS is used, there are common operations
that are performed by all DBMS
Who controls the internet?
  Internet itself has no owners, censors, bosses, board of directors, or  Example:
stockholders o .CA (Canada)
o .UK (Great Britain)
Technology behind the internet o .DE (Germany)
 Standardized communication protocols enable Internet to function o .BIZ (For businesses)
o .COM (Commercial/ Business organizations)
PROTOCOLS o .COOP (For cooperatives)
- agreed on format for doing something o .EDU (Restricted to 4-year degree granting institutions)
- Determine how data will be transmitted between two devices. o .INT (Restricted to organizations that were established by
- The main protocols on which the functioning of the Internet is dependent are international treaty)
referred to as TCP and IP. o .PRO (For professions)
- TCP  Some have more than 1 dot
o allows computers to connect to a network and  Example: peds.nursing.xyz.edu
exchange data  ICANN (Internet Corporation for Assigned Names and
o carries out the task of breaking messages into small Numbers) – created October, 1998
packets o responsible for the technical coordination of the internet;
- IP nonprofit, private sector corporation
o Lower-level protocol
o Responsible for making decisions about the packets Emails
and routing them  One of the most popular uses for the internet
 Has 2 parts, separated by the @ sign: user names and name of the
- Hypertext transmission protocol (HTTP) computer
o Supports the World Wide Web (WWW)  Example: [email protected]
 E-mail communication is different from either telephone or face-to-face
- File Transmission Protocol (FTP) communication.
o Permits users to send all types of electronic files over  Many people have learned the hard way that e-mail is not considered private
the Internet. as is mail delivered by the post office.
- Telnet
o Allows users to access a distant computer as though Use of emoticons and abbreviations
they were sitting in front of it.  To make up for the inability of message recipients to accurately judge the
mood of the sender, the practice of typing characters available on a standard
1. Domain name system keyboard to form a “picture” was begun.
 Give globally unique names to networks and computers  Emoticons/ smileys- small icons to denote a mood
 Benefits:  to make up for the inability of message recipients to accurately judge the
a. Name is easier to remember than the long string of numbers mood of the sender, this practice, typing characters available on standard
b. Name allows change of physical location keyboard to form a picture begun
Paul Mockapetris – pioneer in the protocols that allow DNS to work  Example:
Ex: 166.171.187.117 or www.Google.com ;-) winking
:-( Sad
2. Top Level Domain (TLDs) :-X lips are sealed
 Each country, as of 2003, has a two-letter TLD
  Other less frequently used operating systems include Blackberry, Hiptop,
Basic E-mail Guidelines Linux, and Symbian.
a. Mail on the Internet is not secure.
b. Be careful if you send anything but plain text (also known as ASCII text) as e-
mail.
c. Be cognizant of the size of the e-mail messages and attachments that you
send.
d. Include a signature
e. Do not request a “read receipt” for every e-mail message that you send.
f. Be sure to double-check the “To” and “From” fields prior to sending your Clinical Decision Support Systems
message
g. Do not type in ALL CAPS.
h. Do not type in all lower case
i. Be to the point without rudeness or being abrupt.

Business E-mail Etiquette

a. Sending threatening, slanderous, insubordinate messages is strictly
prohibited.
b. Sending racially and/or sexually harassing messages is strictly prohibited.
c. Pyramid schemes are illegal and should not be transmitted through e-mail.
d. The representation or you as someone else, real or fictional, or a message
sent anonymously is prohibited.
e. Use discretion in using sayings or quotes attached to the signature line.
f. Watch punctuation and spelling.
g. For important items, let senders know you have received their e-mail, even if
you cannot respond in-depth immediately.

Chat and Instant Message

 Use abbreviations, when possible, but only if your reader will understand and if
the e-communication is not formal.
 Smileys, or emoticons, can help convey your intention (for example, being
humorous or sarcastic).

PDA and wireless devices

 The type of operating system determines in part the strategies for
conserving energy in order to prolong battery life
 Desktop, notebook/laptop, tablet and PDA computers may be used as a
stand-alone device or as part of a network.
 The two most commonly used operating systems for PDAs are Palm OS
or Windows mobile.