HEB2201 - Practical 2 - Searching for Information - Generall

8/3/2019 HEB2201 - Practical 2 - Searching for Information - Generall

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SHEB2201 FUNDAMENTALS OF BIOINFORMATICS Associate Professor Khairuddin Itam

PRACTICAL 2

SEARCHING FOR INFORMATION WITH GOOGLE

PART A: LEARNING TO USE GOOGLE

You are given 3 movies:

(a) 01 Introducing Google Basic Searches.wmv(b) 02 Google Special Searches.wmv(c) 03 The Google Toolbar.wmv

Go through each of the movies, one-by-one, in sequence. Follow and understand the steps shown in

the movies on how to use Google effectively. The outcome of this exercise is that I would expect

you to be quite proficient in using Google!

Using your newly acquired experience on the skilled use of Google, do the following exercise:

Look for ALL of the definitions for BIOCOMPUTING. Next, from this list, select 4 (four) of the

most contextually different definitions and enter them into the following table. After you’ve

finished with the definitions for biocomputing, now look for the contextually different definitions

for the words COMPUTATIONAL BIOLOGY and BIOINFORMATICS.

Term Definition Web Address

BIOCOMPUTING

1

the application of computing

to problems in biology,

biochemistry, and genetics

http://dictionary.reference.com/browse/biocomputing

2

systems of biologically

derived molecules that

perform computational

processes

Htttp://Wikipedia.com

3

The design and construction

of computers containing

biological components

http://www.scrabble-word-finder.com/definition-of-biocomputing.html

4

Representing the structure

and function of biological

systems via formal

languages,for description, simulation,

analysis and (eventually)

compilation.

http://lucacardelli.name/BioComputing.htm

After you’ve finished with the definitions for BIOCOMPUTING, now look for the contextually

different definitions for the words COMPUTATIONAL BIOLOGY and BIOINFORMATICS.

Term DefinitionWeb

AddressCOMPUTATIONAL

BIOLOGY

1 Computational biology involves the development and application of data-

analytical and theoretical methods, mathematical modeling and computationalsimulation techniques to the study of biological, behavioral, and social systems

en.wikipedia

.org/wiki/ Computational

_ biology

PRACTICAL 2 - S EARCHING F OR I NFORMATION W ITH GOOGLE Page 1




2

PIC is basic biomedical research at the interface of information

technology and biology.

www.resear ch.ibm.com/

compsci/compbio/

3

Computational biology is an interdisciplinary field that uses the

techniques of applied mathematics, informatics, statistics and

computer science to address biological problems.

http://www.walterjessen.com/computational-biology-and-bioinformatic

s/

4

This course presents an overview of important applications of

computers to solve problems in biology

(analysis of protein and nucleic acid sequences)

http://www.cmu.edu/bio/education/courses/03510/Outline.html

Term Definition Web Address

BIOINFORMATICS

1

is the application of computer science and information

technology to the field of biology and medicine.

http://en.wikipedia.org/wiki/Bioinformatics

2

is the field of science in which biology, computer

science, and information technology merge to form a

single discipline.

http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html

3

Bioinformatics is the analysis of biological information

using computers and statistical techniques; the science of

developing and utilizing computer databases and

algorithms to accelerate and enhance biological research

http://www.roseindia.net/bioinformatics/definition_of_bioinformatics.shtml

4

Typically refers to the field concerned with thecollection and storage of biological information.All matters concerned with biological databasesare considered bioinformatics.

http://kbrin.a-bldg.louisville.edu/~rouchka/HOMEPAGE/definition.html

Discuss on the similarities and differences in definitions among the three words.

Biocomputing Computational Biology Bioinformatics

Similarities

the development of new

database methods to store

genomic information,

computational software

programs, and methods to

extract, process, andevaluate this information;

it also refers to the

refinement of existing

techniques to acquire the

genomic data. Finding

genes and determining

their function, predicting

the structure of proteins

and RNA sequences from

the available DNA

sequence, and determiningthe evolutionary

relationship of proteins

and DNA sequences are

also part of bioinformatics.















the available DNA



















the available DNA






http://en.wikipedia.org/wiki/Computer_science

http://en.wikipedia.org/wiki/Information_technology


http://en.wikipedia.org/wiki/Biology

http://en.wikipedia.org/wiki/Medicine



http://en.wikipedia.org/wiki/Biology

http://en.wikipedia.org/wiki/Medicine

http://en.wikipedia.org/wiki/Computer_science




Differences

the application of

biological models or

processes in structuring

computer programs or

programming; the

emulation of biological

processes or environments

in computer programming

The development and

application of data-

analytical and theoretical

methods, mathematical

modeling and

computational simulation

techniques to the study of

biological, behavioral, and

social systems

Research, development or

application of

computational tools and

approaches for expanding

the use of biological,

medical, behavioral or

health data, including

those to acquire, store,

organize, archive, analyzeor visualize such data.





PART B: LOOKING OUT FOR DATA IN BIOLOGICAL DATABASES

Biological data can be digitized through various methods of input mechanisms, and then stored in

databases. These databases can now be made available to the public, or provided with limited

subscription, or be completely private (no public access at all). The biological data sets can be

accessed through the internet. There are many types of biological data, representing information

from the many domains of biology. Examples of these domains include proteomics, genomics,

biochemistry, physiology, medical and health, biodiversity, plant breeding, animal breeding, genetic

resources and conservation, taxonomy, etc. Most of these data are used as a resource for research,teaching and general knowledge. In a sense, these are knowledge repositories available on-line

24/7.

Using the Google search engine, do a search on the internet for databases that store biological data

from 6 (six) knowledge domains. Ensure that all the 6 biological databases that you’ve selected

contains biological data that are different from the other databases.

Full URL

of Web

Site

http://science.mccneb.edu/pevans/Image_Data_Base/

Biologic

alDisciplin

e

Physiology

Graphicof homepage

Type of

biological data

Plant, plant diseases. Biology of the seed plants

Formatof

biological data

Pictures (*.jpg format) and text only

Comment on

database (Useraccess,layout,

etc)

Cannot do searches. No CD-ROM. Poor interface, navigation





Full URL

of Web

Site

http://www.proteinlounge.com/

Biological

Discipline

proteome

Graphicof home

page

Type of biological data

siRNA, Protein, Peptide Antigen and more.

Formatof

biological data

3D Powerpoint, animations, texts

Comment on


etc)

A unique way to explore the proteome of organisms.

Full URL

of Web

Site

http://csbdb.mpimp-golm.mpg.de

Biological

Discipline

metabolites and proteins





Graphicof home

page


The Plant Subtilase Database, The Golm Metabolome Database

Formatof

biological data

genes, metabolites and proteins

Comment on


etc)

Not much categories

Full URL

of Web

Site

http://www.genecards.org/

Biological

Disciplin

e

Gene, Rna





Graphicof home

page


transcriptomic, genetic, proteomic

Formatof

biological data

Texts, cards, pictures

Comment on


etc)

Very basic and kinda complicated

Full URL

of Web

Site

http://www.bbmri-wp4.eu/node/33

Biological

Disciplin

e

Meta-Databases





Graphicof home

page


Genome, Protein,

Formatof

biological data

text

Comment on


etc)

Good for browsing

Full URL

of Web

Site

http://www.ebi.ac.uk/Databases/

Biological

Disciplin

e

Genome





Graphicof home

page


UniProt, ENA, GOA

Formatof

biological data

Text

Comment on


etc)

Full URL

of Web

Site

http://mi.caspur.it/PMDB/

Biological

Disciplin

e

Protein





Graphicof home

page


Protein, biochemicals

Formatof

biological data

3D, texts

Comment on


etc)

complicated





PART C: MORE GOOGLE EXERCISES

1) The Rosetta Stone is a historically important stone, found in Egypt, that contains cross-

translating text in 3 languages. One of the alphabet text is called the Hieroglyphic, which

reveals the nature of the language used by the ancient Egyptians to communicate.

What are the other two scripts found on the surface of the Rosetta Stone?

Egyptian demotic script, and Ancient Greek

What is the dimension or size of the stone (in metres)?

114.4 centimetres high at its highest point, 72.3 cm wide, and 27.9 cm thick.

0.1144 metres high, .00723 metres wide, and 0.0279 metres thick.

Give the name of the site from where the stone was discovered.

The Rosetta Stone was found in a small village in the Delta called Rosetta (Rashid).

Who was the first person to be able to translate the texts into a modern language?

French Egyptologist called Jean Francois Champollion

Provide an English translation text of the contents of the Hieroglyphic text

In the reign of the young one who has succeeded his father in the kingship, lord of

diadems, most glorious, who has established Egypt and is pious towards the gods,

triumphant over his enemies, who has restored the civilised life of men, lord of the

Thirty Years Festivals even as Hephaistos the Great, a king like the Sun, great king of

the Upper and Lower countries, offspring of the Gods Philopatores, one of whom

Hephaistos has approved, to whom the Sun has given victory, the living image of Zeus,

son of the Sun, Ptolemy, living for ever, beloved of Ptah, in the ninth year, when Aetos

son of Aetos was priest of Alexander, and the Gods Soteres, and the Gods Adelphoi, and

the Gods Euergetai, and the Gods Philopatores and the God Epiphanes Eucharistos;

Pyrrha daughter of Philinos being Athlophoros of Berenike Euergetis; Areia daughter of

Diogenes being Kanephoros of Arsinoe Philadelphos; Irene, daughter of Ptolemy being

Priestess of Arsinoe Philopator; the fourth of the month of Xandikos, according to the

Egyptians the 18th Mekhir. Ptolemy V Epiphanes Eucharistos was born in the 12th or

13th year of the reign of his father, Ptolemy IV. His official birthday was 30th Mesore.

At first associated on the throne with his father he acceeded in the summer of 204 before

1st Mesore (8th September 204), and ruled under the tutelage of a number of regents. He

came of age in the autumn of 197.

Decree: There being assembled the Chief Priests and Prophets and those who enter

the inner shrine for the robing of the Gods, and the Fan-bearers and the Sacred Scribes

and all the other priests from the temples throughout the land who have come to meetthe king at Memphis, for the feast ofthe assumption by Ptolemy, the ever-living, the

beloved of Ptah, the God Epiphanes Eucharistos, the kingship in which he succeeded his

father, they being assembled in the temple in Memphis this day declared:

Whereas king Ptolemy, the ever-living, the beloved of Ptah, the god Epiphanes

Eucharistos, the son of King Ptolemy and Queen Arsinoe, the Gods Philopatores, has

been a benefactor both to the temples and to those who dwell in them, as well as all

those who are his subjects, being a god sprung from a god and goddess (like Horus the

son of Isis and Osiris, who avenged his father Osiris) (and) being benevolently disposed

towards the gods, has dedicated to the temples revenues in money and corn and has

undertaken much outlay to bring Egypt into prosperity, and to establish the temples, and

has been generous with all his own means; and of the revenues and taxes levied in Egyptsome he has wholly remitted and others he has lightened, in order that the people and all

the others might be in prosperity during his reign corn: UK usage-the chief cereal of a

region, in the case of Egypt it refers to wheat, and possibly barley.

and whereas he has remitted the debts to the crown being many in number which they





in Egypt and in the rest of the kingdom owed;

and whereas those who were in prison and those who were under accusation for a

long time, he has freed of the charges against them;

and whereas he has directed that the gods shall continue to enjoy the revenues of the

temples and the yearly allowances given to them, both of corn and money, likewise also

the revenue assigned to the gods from vine land and from gardens and the other

properties which belonged to the gods in his father's time; and whereas he directed

also, with regard to the priests, that they should pay no more as the tax for admission to

the priesthood than what was appointed them throughout his father's reign and until thefirst year of his own reign; and has relieved the members of the priestly orders from the

yearly journey to Alexandria;

and whereas he has directed that impressment for the navy shall no longer be

employed, and of the tax in byssus cloth paid by the temples to the crown he has

remitted two-thirds;

and whatever things were neglected in former times he has restored to their proper

condition, having a care how the traditional duties shall be fittingly paid to the gods;

and likewise has apportioned justice to all, like Hermes the great and great; byssus:

fine linen cloth

and has ordained that those who return of the warrior class, and of others who were

unfavourably disposed in the days of the disturbances, should, on their return be allowed

to occupy their old possessions,

and whereas he provided that cavalry and infantry forces and ships should be sent out

against those who invaded Egypt by sea and by land, laying out great sums in money

and corn in order that the temples and all those who are in the land might be in safety;

the days of the disturbances: By the autumn of 190 Ptolemy IV had recaptured Upper

Egypt from Ankhwennefer.

and having gone to Lycopolis in the Busirite nome, which had been occupied and

fortified against a siege with an abundant store of weapons, and all other supplies

(seeing that disaffection was now of long standing among the impious men gathered into

it, who had perpetrated much damage to the temples and to all the inhabitants of Egypt),and having encamped against it, he surrounded it with mounds and trenches and

elaborate fortifications: when the Nile made a great rise in the eighth year (of his reign),

which usually floods the plains, he prevented it, by damming at many points the outlets

of the channels (spending upon this no small amount of money), and setting cavalry and

infantry to guard them, in a short time he took the town by storm and destroyed all the

impious men in it, even as Hermes and Horus, the son of Isis and Osiris, formerly

subdued the rebels in the same district; and as to those who had led the rebels in the time

of his father and who had disturbed the land and done wrong to the temples, he came to

Memphis to avenge his father and his own kingship, and punished them all as they

deserved, at the time that he came there to perform the proper ceremonies for the

assumption of the crown;and whereas he remitted what was due to the crown in the temples up to his eighth

year, being no small amount of corn and money; so also the fines for the byssus cloth

not delivered to the crown, and of those delivered, the several fees for their verification,

for the same period; and he also freed the temples of (the tax of) the artabe for every

aroura of sacred land and likewise the jar of wine for each aroura of vine land; and

whereas he bestowed many gifts upon Apis and Mnevis and upon the other sacred

animals in Egypt, because he was much more considerate than the kings before him of

all that belonged to the gods; and for their burials he gave what was suitable lavishly and

splendidly, and what was regularly paid to their special shrines, with sacrifices and

festivals and other customary observances; and he maintained the honours of the

temples and of Egypt according to the laws; and he adorned the temple of Apis with richwork, spending upon it gold and silver and precious stones, no small amount; and

whereas he has founded temples and shrines and altars, and has repaired those requiring

it, having the spirit of a beneficent god in matters pertaining to religion;

and whereas after enquiry he has been renewing the most honourable of the temples





during his reign, as is becoming; in requital of which things the gods have given him

health, victory and power, and all other good things.

And he and his children shall retain the kingship for all time. With propitious fortune:

It was resolved by the priests of all the temples in the land to increase greatly the

existing honours of King Ptolemy, the ever-living, the beloved of Ptah, the god

Epiphanes Eucharistos, likewise those of his parents the Gods Philopatores, and of his

ancestors, the Gods Euergetai and the Gods Adelphoi and the Gods Soteres and to set up

in the most prominent place of every temple an image of the ever-living King Ptolemy,

the beloved of Ptah, the god Epiphanes Eucharistos, an image which shall be called thatof 'Ptolemy, the defender of Egypt', beside which shall stand the principal god of the

temple, handing him the weapon of victory, all of which shall be manufactured (in the

Egyptian) fashion; and that the priests shall pay homage to the images three times a day,

and put upon them the sacred garments, and perform the other usual honours such as

given to the other gods in the Egyptian festivals; and to establish for King Ptolemy, the

god Epiphanes Eucharistos, sprung of King Ptolemy and Queen Arsinoe, the Gods

Philopatores, a statue and golden shrine in each of the temples, and to set it up in the

inner chamber with the other shrines; and in the great festivals in which the shrines are

carried in procession the shrine of the god Epiphanes Eucharistos shall be carried in

procession with them.

And in order that it may be easily distinguishable now and for all time, there shall be

set upon the shrine the ten gold diadems of the king, to which shall be added a uraeus

but instead of the uraeus-shaped diadems which are upon the other shrines, in the centre

of them shall be the crown called Pschent which he put on when he went into the temple

at Memphis to perform therein the ceremonies for assuming the kingship: and there shall

be placed on the square surface round about the diadems, beside the aforementioned

crown, golden symbols (eight in number signifying) that it is (the shrine) of the king

who makes manifest the Upper and Lower countries

And since it is the 30th of Mesore on which the birthday of the king is celebrated, and

likewise the 17th of Paophi) on which he succeeded his father in the kingship, they haveheld these days in honour as name-days in the temples, since they are sources of great

blessings for all;

it was further decreed that a festival shall be kept in the temples throughout Egypt on

these days in every month, on which there shall be sacrifices and libations and all the

ceremonies customary at the other festivals (and the offerings shall be given to the

priests who) serve in the temples.

And a festival shall be kept for King Ptolemy, the ever-living, the beloved of Ptah, the

god Epiphanes Eucharistos, yearly in the temples throughout the land from the 1st of

Thoth for five days, in which they shall wear garlands and perform sacrifices and

libations and the other usual honours, and the priests (in each temple) shall be called

priests of the god Epiphanes Eucharistos in addition to the names of the other godswhom they serve; and his priesthood shall be entered upon all formal documents (and

engraved upon the rings which they wear); and private individuals shall also be allowed

to keep the festival and set up the aforementioned shrine and have it in their homes,

performing the aforementioned celebrations yearly, in order that it may be known to all

that the men of Egypt magnify and honour the god Epiphanes Eucharistos the king,

according to the law.

This decree shall be inscribed on a stela of hard stone in sacred [that is hieroglyphic] and

native [that is demotic] and Greek characters and set up in each of the first, second, and

third [rank] temples beside the image of the ever living

2) What are the scientific names of two types of whale?

(1) Physeter macrocephalus,





(2) Balaenoptera musculus

3) Using http://maps.google.com, show a satellite map of the exact position of “Jabatan

Pengangkutan Jalan,Cawangan Kecil Petaling Jaya,Jalan Sultan,46620 Petaling

Jaya,Selangor, Malaysia”

4) Using the same search engine as above, list out the names of roads you need to pass through

when using a car, in order to go from University of Malaya (P.J. Gate) to the JPJ address

above.

University Malaya P.J. Gate

1. Head southwest on Lingkungan Budi

550 m

2. Take the ramp onto Jalan Universiti

700 m

3. Continue onto Jalan Gasing

950 m

4. Turn right onto Jalan Pantai 9/7

550 m

5. Turn left onto Jalan Timur 270 m

6. Slight left onto Jalan Sultan

6 m

7. Slight right to stay on Jalan Sultan





12 m

8. Keep left at the fork

210 m

9. Turn right onto Jalan Yong Shook Lin

550 m

10. Keep right at the fork

150 m

11. Slight left onto Jalan Sultan 28 m

Jalan Sultan

Petaling Jaya, Selangor

Jabatan Pengangkutan Jalan,Cawangan Kecil Petaling Jaya,Jalan Sultan,46620 Petaling

Jaya,Selangor, Malaysia.

Submit your practical assignments within a week, to the Turnitin (SHEB2201 – Practical)

account.

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