KSU - Introduction to Bioinformatics: Research Paper, Mini-Symposium Proceedings 1

Paper Formatting Instructions for Introduction to Bioinformatics

Individual and Team Project Papers for Mini-Symposium Proceedings
J. Q. Author1, P. M. Scriber2, S.E.Writer2
1
Department of Computer Science, Kent State University, Kent, OH
2 Department of Biological Sciences, Kent State University, Kent, OH

Abstract – These instructions give you basic guidelines for
preparing your paper for the Introduction to Bioinformatics
Mini-Symposium Proceedings. Your team papers should be
approximately 4 pages in length. Your individual papers should
also be submitted in this formatting style but there is no length
limitation. Keep in mind that a single page column in this
format will hold approximately the same amount of text as 3
pages in a traditional double spaced 12 pt font document.
Abstracts should not exceed 200 words. Please include
appropriate keywords in your abstract.
Keywords – Margins, fonts, formatting
normal characters for author names and the main text, 9 point
normal characters for the author’s affiliations, and 9 point
bold characters for the Abstract.
2) Format: Use a margin of 25 mm (1”) at the top and 19
mm (3/4”) at the bottom of the page. Left and right margins
should be 19 mm (3/4”). Use a two-column format where
each column is 86 mm (3 3/8”) wide with spacing of 5mm
(1/5”) between columns. Left and right justify your columns.
All figures, tables and equations must be included “in-line”
with the text. Do not use links to external files.

I. INTRODUCTION
Your goal is to simulate, as closely as possible, the
appearance of typeset papers in academic journals or
conference proceedings. This section introduces the reader to
your project and thus address such questions as: “what is the
problem we are addressing?”, “why is this problem
important?”, and “how is your approach different from
previous attempts to solve this problem.?”
II. BACKGROUND
All papers should be submitted electronically in PDF format.
Prepare your papers using a “letter” page size of 8.5x11” or
21.6 x 27.9 mm. If you do not have access to a PDF maker
program please submit your final WORD doc to Dr. Volkert
for PDF formatting.
This section should provide the reader with a brief historical
description of how this problem came to be, who has worked
on this problem before, problems and/or successes of
precious approaches, and background and references to on
any particular specific methods you plan to implement or use
III. METHODOLOGY
This section should clearly explain your methodology,
including any materials, equipment, and/or tools you plan to
use, as well as a description of the source and method for
obtaining your experimental data.
1) Type sizes and typefaces: The best results will be
obtained if your computer word processor has several type
sizes. Try to follow the type sizes specified in Table I as best
you can. Use 16 point bold character for the title, 10 point
IV. RESULTS
This section should clearly describe the results of your work.
Tables and graphs are often included in this section. Keep in
mind that your result should be reproducible, so be sure you
have included enough information in your paper to enable
someone to retrace you steps.
A. Figures and Tables
Position all figures and tables at the tops and bottoms of
columns. Avoid placing them in the middle of columns.
Large figures and tables may span across both columns (see
fig. 2 for an example of a column spanning figure). Figure
captions should be below the figures and table captions
should be centered above the tables. Refer to Table I, and fig
1., fig. 2., and fig. 3. as examples of proper table and figure
placement (i.e. you may place large figures or tables across
both columns but they should be at the top or bottom of page
boundaries).
TABLE I. TYPE SIZES FOR CAMERA-READY PAPERS
Type 1. Appearance
Size
8 Table captions (bold caps), figure captions
(bold and centered or fully justified)
9 Author affiliations, abstract, references
10 Authors, Section Titles (bold caps),
Subsection Titles (italics) main text.
16 Title (bold)
Use the abbreviation “fig 1.” when referring to figures in
your text and “Fig 1.” at the beginning of a sentence. Figure

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KSU - Introduction to Bioinformatics: Research Paper, Mini-Symposium Proceedings
(a)
Figure 1: Image (a) shows a histogram of the grey scale values present in an acquired image containing a sample of bovine sperm. For different
samples the sperm may be represented by grey scale values ranging from 0 to 140 depending on a variety of experimental conditions. Image (b)
shows a histogram of the pixel grey scale values in the same image after application of the filters described in the text. All sperm in the image have at
least a single pixel with the lowest possible grey scale value, zero.
labels should be legible, about 8-point type. Fig 2. is an
example of a figure containing pseudo code. Note that the
font is changed to courier, which is a non-proportional font.
Multipliers can be especially confusing in scientific papers.
Write “Magnetization (kA/m)” or Magnetization (103 A/m)”
to ensure that the reader knows exactly what your scale is.
B. References
Number citations consecutively in square brackets [1]. The
sentence punctuation follows the brackets [2]. Refer simply
to the reference number, as in [3]. Do not use “Ref [3]” or
reference [3]” except at the beginning of a sentence:
“Reference [3] was the first…”. You are strongly encouraged
to use the demo ENDNOTE software for compiling your
references, but this is not a requirement.
Pseudo code:
INITIALIZE_CELLS();
EVALUATE_CELLS();
BEGIN_LOOP
NOURISH_CELLS(number,%A,%T,%C,%G);
SPLIT_CELLS();
MUTATE_CELLS();
EVALUATE_CELLS();
REPEAT UNTIL(TERMINATION_CHECK()==TRUE)
Figure 2: Cell cycle pseudo code.
Number footnotes separately in superscripts (Insert |
Footnote).1 Place the actual footnote at the bottom of the
1
It is recommended that footnotes be avoided (except for the unnumbered
footnote with the receipt date on the first page). Instead, try to integrate the
footnote information into the text.
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(b)
column in which it is cited; do not put footnotes in the
reference list (endnotes).
Please note that the references at the end of this document are
in the preferred referencing style. Give all authors’ names; do
not use “et al.” unless there are six authors or more. Use a
space after authors' initials. Papers that have not been
published should be cited as “unpublished” [4]. Papers that
have been submitted or accepted for publication should be
cited as “submitted for publication” [5]. Please give
affiliations and addresses for personal communications [6].
Capitalize only the first word in a paper title, except for
proper nouns and element symbols. If you are short of space,
you may omit paper titles. However, paper titles are helpful
to your readers and are strongly recommended. For papers
published in translation journals, please give the English
citation first, followed by the original foreign-language
citation [7].
C. Abbreviations and Acronyms
Define abbreviations and acronyms the first time they are
used in the text, even after they have already been defined in
the abstract. Abbreviations such as IEEE, SI, ac, and dc do
not have to be defined. Abbreviations that incorporate periods
should not have spaces: write “C.N.R.S.,” not “C. N. R. S.”
Do not use abbreviations in the title unless they are
unavoidable (for example, “IEEE” in the title of this article).
V. DISSCUSION
This section should compare and contrast your result and
your project approach with previous work in the area and
highlighting the scientific contribution of your work. For
example, if you results were or were not what you anticipated
suggest some appropriate follow-up experiments. Another
example, discuss why your approach improves on or extends
KSU - Introduction to Bioinformatics: Research Paper, Mini-Symposium Proceedings
the results from a previous published approach to the same or
a similar problem.
NOTE: you may also consider combining the two previous
sections into one section entitled Results & Discussion. In
this case you would intersperse your discussion with each of
your results.
A. Other Recommendations
Use one space after periods and colons. Hyphenate complex
modifiers: “zero-field-cooled magnetization.” Avoid dangling
participles, such as, “Using (1), the potential was calculated.”
[It is not clear who or what used (1).] Write instead, “The
potential was calculated by using (1),” or “Using (1), we
calculated the potential.”
Use a zero before decimal points: “0.25,” not “.25.” Use
“cm3,” not “cc.” Indicate sample dimensions as “0.1 cm ×
0.2 cm,” not “0.1 × 0.2 cm2.” The abbreviation for “seconds”
is “s,” not “sec.” Do not mix complete spellings and
abbreviations of units: use “Wb/m2” or “webers per square
meter,” not “webers/m2.” When expressing a range of values,
write “7 to 9” or “7-9,” not “7~9.”
A parenthetical statement at the end of a sentence is
punctuated outside of the closing parenthesis (like this). (A
parenthetical sentence is punctuated within the parentheses.)
In American English, periods and commas are within
quotation marks, like “this period.” Other punctuation is
“outside”! Avoid contractions; for example, write “do not”
instead of “don’t.” The serial comma is preferred: “A, B, and
C” instead of “A, B and C.”
1000000
Figure 3: Mutation rate with equal nutritional distribution
If you wish, you may write in the first person singular or
plural and use the active voice (“I observed that ...” or “We
observed that ...” instead of “It was observed that ...”).
Remember to check spelling. If your native language is not
English, please get a native English-speaking colleague to
proofread your paper. 100000
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VI. CONCLUSION
The word “data” is plural, not singular. The subscript for the
permeability of vacuum µ0 is zero, not a lowercase letter “o.”
The term for residual magnetization is “remanence”; the
adjective is “remanent”; do not write “remnance” or
“remnant.” Use the word “micrometer” instead of “micron.”
A graph within a graph is an “inset,” not an “insert.” The
word “alternatively” is preferred to the word “alternately”
(unless you really mean something that alternates). Use the
word “whereas” instead of “while” (unless you are referring
to simultaneous events). Do not use the word “essentially” to
mean “approximately” or “effectively.” Do not use the word
“issue” as a euphemism for “problem.” When compositions
are not specified, separate chemical symbols by en-dashes;
for example, “NiMn” indicates the intermetallic compound
Ni0.5Mn0.5 whereas “Ni–Mn” indicates an alloy of some
composition NixMn1-x.
Be aware of the different meanings of the homophones
“affect” (usually a verb) and “effect” (usually a noun),
“complement” and “compliment,” “discreet” and “discrete,”
“principal” (e.g., “principal investigator”) and “principle”
(e.g., “principle of measurement”). Do not confuse “imply”
and “infer.”
Prefixes such as “non,” “sub,” “micro,” “multi,” and “"ultra”
are not independent words; they should be joined to the
words they modify, usually without a hyphen. There is no
period after the “et” in the Latin abbreviation “et al.” (it is
also italicized). The abbreviation “i.e.,” means “that is,” and
the abbreviation “e.g.,” means “for example” (these
abbreviations are not italicized).
REFERENCES
[1] Bruno, W.J., Socci, N.D., and Halpen, A.L. Weighted
Mutation R
neighbor-joining: A likelihood-based approach to distance-based
phylogeny reconstruction. Molecular Biology and Evolution, 2002.
17:189-197.
[2] Chothia, C. and Lesk, A.M. The relation between the
divergence of sequence and structure in proteins. EMBO Journal,
1986. 5: 823-826.
[3] Goad, W. Computational analysis of genetic sequences. Ann.
Rev. Biophys. Biophys. Chem., 1986. 15:79-95
[4] Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K. and
Watson J.D. Molecular Biology of the Cell. Garland Publishing,
New York and London, 1989.
[5] Bishop and Rawlings (eds) Nucleic acid and protein sequence
analysis: A practical approach. IRL Press, Oxford, 1987.
[6] Schmidt, U., Begley, C. Cancer diagnosis and microarrays. The
International Journal of Biochemistry and Cell Biology. 2002. 35
(2): 119-124.
[7] Upal, M.A., and Neufeld, E. Comparison of unsupervised
classifiers. In Proc. of the First International Conference on
Information, Statistics and Induction in Science. World Scientific,
Singapore. 1996. 342-353.