LaTeX Introduction 4: Simple Math 2

This tutorial is still on simple mathematical expression. Processing document using Latex is very different from using proprietary word processing software which is based on GUI (Graphical User Interface). Using Latex, what you see in winEdt is not the final result you will get. Always compile the document after you make make any change and see the result.

Try this template first and after that do make exploration by yourself.


\documentclass[11pt]{article}

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{latexsym}

\setlength{\textwidth}{16cm}
\setlength{\hoffset}{-2cm}
\setlength{\textheight}{24.5cm}
\setlength{\voffset}{-2cm}

\setlength{\parindent}{0cm}
\addtolength{\parskip}{2mm}

\newcommand{\R}{\mathbb{R}} % What is this ?

\pagestyle{empty}

\begin{document}

\leftline{{\bf Demo 4 \hfill LEARNING \LaTeX{}}} % Header for first page different way with demo 3

\medskip % This is for medium skip

\leftline{{\bf 2008 -- 2009}}

\bigskip

\centerline{\bf Demo \LaTeX{} 4}

\bigskip

\subsection*{Some common mistakes}

\begin{itemize}
\item Always put numerals in math mode. Thus, do $27.3$, not 27.3.
\emph{When you have numerals like 27.3 in emphasized text, you usually want them in roman,
like $27.3$, not emphasized.} Also, a negative number, -273, will look wrong if left in
text mode. In math mode you get a proper minus sign $-273$.

When giving a range, $200-300$ will look like a subtraction. Here you can do
$200$-$300$ if you prefer. Notice the difference in the various dashes:
one dash is $200$-$300$, two dashes is $200$--$300$, three dashes is
$200$---$300$.

For numerals with units you can do $42\text{km}^2$.

\item Avoid blank lines around displays. Thus do not do
\begin{verbatim} % Hurufnya verbatim dan menampilkan apa adanya tanpa mengeksekusi perintah
For $W_1 = \{(q_1,\,0,\,0,\,0)\st q_1\in\R\}$ we have

$$
W_1^\perp = \{(q_1,\,q_2,\,0,\,p_2)\st q_1, q_2, p_2\in\R\}.
$$

For $W_2 = \{(q_1,\,q_2,\,0,\,0)\st q_1,q_2\in\R\}$ we have
% baris kosong tidak boleh
$$
W_2^\perp = \{(q_1,\,q_2,\,0,\,0)\st q_1, q_2 \in\R\} = W_2.
$$
\end{verbatim}
If you want to `set off' displays in your tex file, do this:
\begin{verbatim}
For $W_1 = \{(q_1,\,0,\,0,\,0)\st q_1\in\R\}$ we have
% % Untuk menampilkan spasi kosong hendaknya pakai % saja jangan dibiarkan kosong
$$
W_1^\perp = \{(q_1,\,q_2,\,0,\,p_2)\st q_1, q_2, p_2\in\R\}.
$$
%
For $W_2 = \{(q_1,\,q_2,\,0,\,0)\st q_1,q_2\in\R\}$ we have
%
$$
W_2^\perp = \{(q_1,\,q_2,\,0,\,0)\st q_1, q_2 \in\R\} = W_2.
$$
\end{verbatim}
\end{itemize}


\end{document}

LaTEX Introduction 3: Section and subsection

It is relatively easy to handle structure of document in LaTEX especially on section and sub section management. Try the following template and do make self experiment.

\documentclass[11pt]{article}

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{latexsym}

\setlength{\textwidth}{16cm}
\setlength{\hoffset}{-2cm}
\setlength{\textheight}{24.5cm}
\setlength{\voffset}{-2cm}

\setlength{\parindent}{0cm}
\addtolength{\parskip}{2mm}

\begin{document}
\leftline{\textbf{Demo LaTEX 3}\hfill \textbf{2008 -- 2009}} % print the left and right text

\begin{center}
\Large\textbf{Demonstration 3: Sections and Sub Sections}
\end{center}

\bigskip

% \section*{Introduction}

\section{Basic definitions and examples}
One more advantage of LaTEX is in section and subsection handling. This is section 1. You do not need to print number of chapter and LaTEX will set it automatically.


\section{First results}
This is section 2.

\subsection{The situation in the 20th century}
This subsection 2.1

\subsection{Recent developments}
This is subsection 2.2

\section{More results}

This is section 3

\section{Concluding Remarks}
This is section 4
% \tableofcontents


\end{document}

LaTEX Introduction 2: Simple Math

LaTEX is like a programming language. When you make document with LaTEX it is like you make a program. One of adavantages of LaTEX compared to other word processing softwares (especially a proprietary word processor) is its flexibility in mathematics formula writing. Of course, it is not trivial for beginners. In my experience, I need about 3 hours to make a very simple document with very basic mathematical expression.

There are a lot of sources on LaTEX in the internet. Just type a keyword on LaTEX in your search engine and then you will find abundance materials. If you just started and enjoy an example-based study, try this template and then do make an experiment by yourself.


% PREAMBLE (APPLIES TO WHOLE DOCUMENT) :
\documentclass[11pt]{article}

\usepackage{amsmath} % THESE THREE LINES SHOULD
\usepackage{amssymb} % BE KEPT IN EVERY DOCUMENT
\usepackage{latexsym} % YOU WRITE DURING THIS COURSE

\setlength{\textwidth}{16cm}
\setlength{\hoffset}{-2cm}
\setlength{\textheight}{24.5cm}
\setlength{\voffset}{-2cm}

\setlength{\parindent}{0cm}
\addtolength{\parskip}{2mm}

% END OF PREAMBLE

\begin{document}

\begin{center}
\textbf{Demonstration 2: Simple maths, 2008 -- 09}\\[3mm]
\today
\end{center}

\bigskip
% $ $ is for mathematical function
% ----- is for membuat tanda garis atau
% $-$ adalah tanda minus
% emph is for cetak miring
% int is for integral function
% | | is for absolute
% $$ for function

In the peptide identification using PMF, first of all, the sample was seeded in the Mass Spectrometry (MS) and then its mass spectrometric data was processed. The general processing steps are baseline (background) substraction, noise removal, peak picking, peak clustering, and de-isotoping. The data output of those steps is a peptide candidate list. This candidate list then will be compared to the database. The main key of the protein identification is the accuracy to produce peptide candidate list and time spent in database comparison. This report will use new approach. The theoretical spectrometric data will be developed based on the true peptide list after that is compared to real spectra data gotten from experiment. By using this approach the data processing which will be applied to experimental spectra data is only baseline (background) substraction.

The probability of isotope's position can be estimated by using Poisson distribution. The first peak is always assumed as monoisotope peak and then the adjacent peak with distance 1+error will be member of the group. This method also has been implemented in programmable computer systems, Field Programmable Gate Array, based.
$$
E(i,m_p)=\frac{a_p\,F(m_p)^i}{i!}; i=1,2,3,\ldots; E(i,m_p)>0, % Poisson Distribution for peptide
$$
and
$$
F(m_p)=0.000594\,m_p-0.03091,
$$
where $F(m_p)$ is maaping function of $m_p$, $E(i,m_p)$ is intensity of $i$-th, $m_p$ is monoisiotopic mass, $a_p$ is a monoisiotopic intensity at $m_p$,and $i$ is number of isotope in one cluster.

\end{document}

Word Processing: LaTEX Introduction (1)

LaTEX is one of open-source word processing which is very powerful and very convenient. Like with other new softwares, if we use for the first time, we need time to learn and accustomized with it. However, once we have use it, it will be much easier and give us independence of our document processing.

For the beginning just try this template. Offcourse you need LaTEX compiler software and winEdt for editing it.

% START OF PREAMBLE
\documentclass[11pt]{article}

\usepackage{amsmath} % These three rows should be kept
\usepackage{amssymb} % in every document
\usepackage{latexsym} % To use latex symbol font.

\setlength{\textwidth}{16cm} % original: 16, this is width of txt
\setlength{\hoffset}{-2cm} % Horizontal offset: distance of text from tepi kertas
\setlength{\textheight}{24.5cm} % original: 24.5
\setlength{\voffset}{-2cm} % Vertical offset: Jarak antara tulisan dengan tepi kertas

\setlength{\parindent}{0cm}
\addtolength{\parskip}{2mm} % Line spacing for new pharagraph

% END OF PREAMBLE


\begin{document} % Begin for whole Document

\begin{center} % Begin for judul: center means ditengah
Demonstration 1: Text, Graduate Year 2008 -- 09
\end{center} % End for judul

Since Mass Spectrometry replaced 2 Dimensional Electrophoresis (2DE) method, the development of proteomics research is much more rapid. The main aims of proteomics are protein identification and quantification. Initially research in proteomics was limited only for peptide identification. Further steps, the research also include protein profiling and its quantitation. Quantitative proteomics is a powerful tool to study the relative change of the same peptide which was treated in different condition. The current emerging of Mass Spectrometry (MS) technology especially on its resolution, accuracy, and speed, has been made quantitative proteomics more powerful to be used in wide proteome analysis. However the outcome data of MS is only spectra, not directly quantitative.



\end{document} % End for whole document

Computational Proteomics

Here are some fundamental abbreviations in computational proteomics:

PMF = Peptide mass Fingerprinting

LC = Liquid Chromatography

MS = Mass Spectrometry

MALDI = Matrix Assisted Laser Desorption Ionization

TOF = Time of Flight

SILAC = Stable Isotope Labelling with Amino Acid in Cell Culture

HUPO = Human Proteome Organization

PSI = Protein Standardization Initiative

PEDRO = Proteomics Experimental Data Repository

XML = eXtensible Markup Language

PEML = Proteomics Experiment Markup Language

LIMS = Laboratory Information Systems

PERL = Practical Extraction and Report Language

CSS =Cascading Style Sheet

SQL = Structure Query Language

HTML = Hypertext Transfer Markup Language

CSS = Cascading Style Sheets

XSLT = XML Stylesheet Language Transformations

SVG = Scalable Vector Graphics

GPMDB = Global Proteome Database

Making Bibliography

Do you have an essay assignment to be completed and submitted ?. Are you bothered with bibliography ?. So check it out tutorial on annotated bibliography below.

Annotated bibliography

Introduction

Purpose of this module:

To help you understand what is required when compiling an annotated bibliography as part of your assessment.

Learning objectives:

By taking this tutorial, you will be able to:

• demonstrate an understanding of what constitutes a good annotated bibliography
• recognise the importance of referencing correctly
• show evidence that you can apply good evaluation criteria in the selection of sources to include in your bibliography
• show evidence that you can apply critical thinking skills when writing annotations

What is an annotated bibliography

A bibliography is an alphabetical listing of books. They are generally included at the end of an article, chapter or book, to reference those works which the author referred to during the research and writing process. Bibliographies should include any source used whether books, journal articles, reports, electronic materials such as web sites, video or audio recordings.

A bibliography details the citation information for each source: author(s), date of publication, title, and publisher's name and location, including journal title, volume part and page numbers for journal articles. Further information such as the URL (web address) and/or format is required for non print materials. The exact layout of each entry is determined by the citation style used. One of the functions of a bibliography is to enable the reader to find the sources used in the writing of the piece and therefore accuracy is essential.

An annotated bibliography can be defined as a list of works on a particular topic, with each entry accompanied by a note (i.e. an annotation) intended to describe, summarise, and evaluate each source included.

The content of an annotated bibliography may vary depending on its purpose. It may:

• review the literature of a particular subject;
• demonstrate the quality and depth of reading that you have done
• exemplify the scope of sources available—such as journals, books, web sites and magazine articles;
• highlight sources that may be of interest to other readers and researchers;
• emphasise and organise sources for further research.

Why write an annotated bibliography?

Writing an annotated bibliography is excellent preparation for a research project. It tests your understanding of the key literature for your topic, and where each source fits into your own research question. It also enables you to highlight where there are research questions still to be answered and thus to put your own thesis into context.

By writing annotations for each source, you have to critically read and select, summarise the main points, evaluate the quality of each piece of research and consider what you have read from your own perspective.

Each annotation should be more than a mere description and more than just a summary of the main conclusions although these are important elements. Each entry should also include an evaluation of the source and an assessment of its usefulness to your research topic. It therefore requires a critical analysis of the overall literature on your topic, a selection of the ‘key’ sources and your own personal reflection on how these have added to your thinking. The annotation should normally be objective rather than subjective.

By reading and responding to a variety of sources on a topic, you can see what issues are involved, what the current thinking is in your field and then develop your own arguments and point of view. It will also assist you in writing the literature review required for your degree.

How do I write an annotated bibliography?

Decide on the Focus of bibliography

You first need to decide on the focus for your annotated bibliography. This will generally be the same as the focus of your research topic but this is not essential. Define the scope of your bibliography carefully so that you can make good judgments about what to include and exclude. You need to be reasonably comprehensive but keep within well-defined boundaries to fit within the overall word count required. You will need to read more widely than just the items you select for inclusion to ensure you have chosen the key material. This involves continually refining your focus as you proceed.

Search the relevant subject databases, open access journals and institutional repositories covering your topic.

For help on searching databases use the tutorials Bibliographic Databases and Successful Database Searching. For help on searching open access journals and institutional repositories use http://www.shef.ac.uk/library/cdlists/articles.html Locate and record citations to books, periodicals, and other documents that may contain useful information and ideas on your topic. Be accurate and write down all the information you need to include in the citation. Use a reference management system such as Endnote.

Select your sources carefully

Briefly examine and review the actual items. Then choose those works that provide a variety of perspectives on your topic and read these in more depth. Keep the following questions in mind to help when selecting the sources and writing your annotations.

• What specific topic/ problem am I investigating?
• What research question(s) am I exploring? What is the overall aim of my research? Has my aim altered, and become more focused through using particular sources?
• What type of information sources do I need for my research? Am I looking for journal articles, reports, policies or primary historical data?
• How does each individual text relate to my research topic and add to my thinking? How can I justify its inclusion in the annotated bibliography?
• What are the essential or key texts on my topic? Am I finding them? How do I know they are the essential texts? Are the sources cited frequently by other authors?
• Is it a reliable and current source? Is the research biased or objective? Who is the author? What are his/her credentials?
• What question(s) does each source investigate? How effective is the research method used? How good is the evidence? Do you draw the same conclusions from the evidence presented?
• Has the author developed a logical argument; identified any flaws or weaknesses in their research; made relevant connections or links across topics, themes and disciplines, or linked theory to practice?

For additional help on Evaluating Information use appropriate tutorial

Critical writing skills

Your aim should be to convince your reader us that you understand where each source fits into your research proposal. Ask yourselves the following questions:

• Is your research topic clearly stated? Is it in focus throughout each annotation?
• Does your reasoning on the value of each source lead to a logical conclusion?
• Do you state and defend your assumptions?
• Is your position well-informed?
• Are your evaluations sound?
• Are your sources the leading research for your field? Are they credible?
• Have you generalised too much or been too specific too soon?
• Have you covered alternative views?
• Are you being fair and open-minded?
• Will your annotated bibliography convince your reader?
• Is your writing clear and concise?

Based on Ennis, R.H. (2006) Critical thinking skills. Available from: http://faculty.ed.uiuc.edu/rhennis/

Tips (from UNSW)

• Each annotation should be concise. Do not write too much—remember, you are writing a summary, not an essay. Annotations should not extend beyond one paragraph unless otherwise stipulated in your assignment guidelines. As this is not an extended piece of writing, only mention significant and relevant details
• Any information apparent in the title of the text or journal can be omitted from the annotation.
• Background materials and references to previous work by the same author usually are not included. As you are addressing one text at a time, there is no need to cross reference or use in-text citations to support your annotation.
• Unless otherwise stipulated, you should write in full sentences using academic vocabulary.

Reporting words

It is sometimes challenging to find the vocabulary in which to summarise and discuss a text. Here is a list of some verbs for referring to texts and ideas that you might find useful:

account for	clarify	describe	exemplify	indicate	question
analyse	compare	depict	exhibit	investigate	recognise
argue	conclude	determine	explain	judge	reflect
assess	criticise	distinguish	frame	justify	refer to
assert	defend	evaluate	identify	narrate	report
assume	define	emphasise	illustrate	persuade	review
claim	demonstrate	examine	imply	propose	suggest

Click on the links above for a definition of the verbs given in the Compact English Dictionary available from AskOxford.com

Adapted from the University of Toronto (2008) Writing an Annotated Bibliography. Available from: http://www.utoronto.ca/writing/annotatebib.html

Guidelines for annotations

In the sample annotation below, each element is numbered (see Key):

(1) Trevor, C.O., Lansford, B. and Black, J.W., 2004, 'Employee turnover and job performance: monitoring the influences of salary growth and promotion', Journal of Armchair Psychology, vol 113, no.1, pp. 56-64.

(2) In this article Trevor et al. review the influences of pay and job opportunities in respect to job performance, turnover rates and employee motivation. (3) The authors use data gained through organisational surveys of blue-chip companies in Vancouver, Canada to try to identify the main causes of employee turnover and whether it is linked to salary growth. (4) Their research focuses on assessing a range of pay structures such as pay for performance and organisational reward schemes. (5) The article is useful to my research topic, as Trevor et al. suggest that there are numerous reasons for employee turnover and variances in employee motivation and performance. (6) The main limitation of the article is that the survey sample was restricted to mid-level management, (7) thus the authors indicate that further, more extensive, research needs to be undertaken to develop a more in-depth understanding of employee turnover and job performance. (8) This article will not form the basis of my research; however it will be useful supplementary information for my research on pay structures.

Key:

(1) Citation
(2) Introduction
(3) Aims & Research methods
(4) Scope
(5) Usefulness (to your research/ to a
particular topic)
(6) Limitations
(7) Conclusions
(8) Reflection (explain how this work
illuminates your topic or how it will fit
in with your research)

Now test your understanding of annotating a bibliography by taking the drag and drop quiz.

Summary

You have now finished this tutorial!

Having worked through this tutorial you should now be able to:

• demonstrate an understanding of what constitutes a good annotated bibliography
• recognise the importance of referencing correctly
• show evidence that you can apply good evaluation criteria in the selection of sources to include in your bibliography
• show evidence that you can apply critical thinking skills when writing annotations

To revise anything, click on the relevant link on the left-hand side in the Content Menu to be taken to that page.