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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27316?offset=1050</link>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21453/ra-research-associate-bioinformaticscomputational-biologist</guid>
  <pubDate>Thu, 26 Feb 2015 03:44:24 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA / Research Associate Bioinformatics/Computational Biologist]]></title>
  <description><![CDATA[
<p>The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067 </p>

<p>RA / Research Associate (Bioinformatics/Computational Biologist) <br />Salary: Rs. 23000/- + HRA <br />Vacancy: 1 <br />Essential Qualifications: PhD, preferably in plant biotechnology/biochemistry/Bioinformatics with experience in analyzing high throughput omics-based data. Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, managing the project portal, preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.</p>

<p>Address:	Prof Indira Ghosh, room #12 Project Investigator, (Core Metabolomics) School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067.</p>

<p>Apply Details	<br />Last Date: March 3rd 2015 <br />Web/Notification URL	http://www.jnu.ac.in/Career/currentjobs. htm</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/21096/how-to-prepare-your-bioinformatics-cv</guid>
	<pubDate>Mon, 09 Feb 2015 01:50:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/21096/how-to-prepare-your-bioinformatics-cv</link>
	<title><![CDATA[How to Prepare your Bioinformatics CV ?]]></title>
	<description><![CDATA[<p>Preparing a CV is also an art as well as a requirement for a person applying for a job .<br /> Curriculum Vitae is the first impression on the employer so it should be the best.How It can be the best can be learnt.Here is a link where you can get guidelines on how CV can be prepared and a sample also. Preparing your own Curriculum Vitae can seem a daunting task, quite apart from what to put in and what to leave out, describing your own strengths and abilities isn't easy. What we have tried to do with the following guidelines is to make the whole process a much easier one and ensure that you end up with a professional document which shows you how to pitch your skills and stand out from the crowd. In the current economic and employment climate, employers are looking to consistently improve on productivity and match a prospective employee's skills and experience with the job needs, both now and in the future.<br /> <strong><br /> Presentation and layout</strong><br /> Always ensure that your CV is laser-printed on white, good quality paper, use a clean typeface and don't go smaller than 12 point.<br /> The use of sub-headings (e.g. Personal details, career history, etc.) will help potential employers glean the information they require with ease.<br /> There should be clear spaces between category headings for easy clarification and definition.<br /> Your name, address and phone number(s) should form the start of the document. If you are giving a work number add the following - 'please use with discretion.'<br /> Commencing with your present or most recent employer, state your career history. Then list your professional qualifications. If you have been working for many years list your academic qualifications and a very brief mention as to your college or schooling.<br /> If you are just commencing your working life, having previously been a student, provide more in depth knowledge regarding your academic achievements to date.<br /> <br /> <strong>Content</strong></p><p>Starting with your current or most recent employment provide details of your position as follows:</p><ul>
<li>A chronological CV should be arranged in reverse chronological order. It should be apparent immediately where you are now.</li>
<li>Remember that an application form is limited to the few things that a particular institution wants to know about everybody. A CV lets you give information that is unique to you. Add all your key accomplishments and activities in the initial draft. In subsequent drafts, you can remove information that may not be pertinent.</li>
<li>Resist the temptation to append explanatory sentences or language, which will distract the reader from the basic information being presented. The language of a CV is abbreviated and succinct. When applying for residency training, you will have the opportunity to express yourself in a personal or biographical statement. In the future, when applying for a job or some other type of position, you will want to include an appropriate cover letter with your CV to explain your particular qualifications and strengths for the position.</li>
<li>Don&rsquo;t despair if your CV doesn&rsquo;t resemble those of other students who are applying to the same residency program. Everybody&rsquo;s CV is different. Even if everyone used the same format suggested in this section, your CV will not resemble others&rsquo; because it doesn&rsquo;t have the same content. No residency program director is looking for a specific CV style. You will receive points for neatness, and readability.</li>
<li>Be honest. If you haven&rsquo;t accomplished anything in a particular category, leave it out. Don&rsquo;t create accomplishments to fill in the spaces. You can be specific about your level of participation in a project or activity, but don&rsquo;t be misleading (i.e., you can say you coordinated membership recruitment for your AMSA chapter, but don&rsquo;t say you were &ldquo;president&rdquo; unless you were).</li>
</ul><ul>
<li>Job title - time that you have held this position</li>
<li>The key tasks and responsibilities that comprise this role's requirements - notable achievements whilst in the role</li>
<li>Where possible quantify your achievements with precise facts and figures, e.g. managed junior staff, handled department budget, prepared management reports</li>
<li>Expand on the skills you are using in your current job which you believe will be valuable in the position(s) for which you are applying</li>
</ul><p>It is not necessary to state the reason you are leaving your current position. This will be a topic for conversation when you are invited for interview or can be covered in your letter of application.<br /> For all previous employment, unless one appointment was more significant than your current or last position, keep details brief i.e. the name of the company, job title, period of employment and the job.<br /> Be sure there are no gaps in your career history - unless for example you took a year out to travel, in which case make reference to this under Interests/Hobbies.<br /> If you are a student just starting work, give any evidence you can to demonstrate your practical skills e.g. school prefect, event organisation, member of sports team, contributor to college magazine or voluntary work.<br /><br /> You are under no obligation to disclose marital status, age or whether or not you have children unless these are specific criteria for selection for a position that you are interested in.<br /> Consider what examples (interests/ hobbies) you can give to show that you match the selection criteria.<br /><br /> If they want someone to work as part of a large team, remember to say if you belong to a local organisation or if you are part of a sports team.<br /><br /> If they want someone who will work on their own for large periods of time, make reference to an Open University course you are considering undertaking.<br /><br /> Your primary objective is to convince the prospective employer that you have the requisite skills, experience and hunger to do the job.<br /><br /> Your CV should be no more than two A4 pages and as every employer is different remember to customise your CV to every job you go after.</p><p>There are abundant books on the contents and presentation of a general CV. A BMJ article published in 1978, offering doctors guidance on how to prepare a CV, has been reprinted in the widely read How to do it series.1 2 A survey among postgraduate deans and training advisers at regional colleges found that the contents and presentation of a model CV for doctors in training has been published.3 It is perhaps surprising to note that these models differ significantly from one another. Although they may be useful as starting points, their differences tend to create confusion and anxiety among students. I would argue that these differences exist because the content and presentation of the "ideal" CV vary considerably among individual applicants, the stage of their careers, and the purposes for which the CV is used. It is impossible to create a generic CV. I have therefore not attempted to draw up another model CV. Rather, the purpose of this article is to outline the general principles and important practical points in preparing a good CV. General principles on contents Before finalising your CV for a particular purpose you must be sure of your objectives, whether it is used as an initial screening or the only selection instrument, and the criteria against which it is judged. What details, and how many of them, to include in your CV depends on these factors. I shall illustrate with examples relevant to medical students.&nbsp;<br /> <br /> (1) Job application Your objective is to get the job. In a job application, the CV is used for two purposes: as an initial screening instrument for shortlisting candidates and as a framework for discussion during the interview. The explicit criteria used for shortlisting are usually given in the job advertisement. For some organisations, separate lists of essential and desirable criteria are given. Alternatively, you can get a good idea of the basic requirements from the job description. Your CV must clearly highlight these criteria, preferably on the first page. These usually include: formal qualifications; registration with the General Medical Council; and the prescribed experience. It is sometimes easy to forget to mention items specifically asked for in the job description (for example, a valid driving licence). The implicit criteria are less easy to pinpoint. For example, how much detail on your BSc dissertation and publications should you include? Should you make a long list of extracurricular activities, interests outside medicine, and positions of responsibility? If you admit to a wide range of extracurricular activities and interests, would you be considered as a candidate with a well balanced mature personality or will it be interpreted to mean that you will have little time or interest to do your job? There are no easy answers. Common sense might tell you that BSc dissertation and publications are more important in application for teaching hospital or research posts, but less important for district hospital posts. Conversely, you might think that interests outside medicine are more important for posts in district hospitals or in general practice. This is, however, not always true. A few consultants at district hospital are highly academic. Information gathered from students and doctors working under the professor or consultant concerned may be vital. Alternatively, it is worth while doing your homework by looking up your prospective consultant in the medical directory. This may occasionally prompt you to include information that you might otherwise have left out. For example, you may find that the consultant qualified in Scotland and has previously worked in Scotland for a considerable time, and you may decide to add in your CV that you studied in a Scottish secondary school. Since the CV is only used as for initial screening, you need not go into your previous experience or extracurricular activities in too much detail. Highlight only the most significant points, and leave the details for the interview. If you are applying for a clinical post, one of your referees should be a consultant for whom you have worked as a student. You should ask for permission to use his/her name before submitting your application.&nbsp;<br /> <br /> (2) Application for research scholarship or PhD studentship The CV and application form are sometimes used as the sole selection instrument, and you must make enquiries before you submit your application. Clearly, academic ability is the main criterion for selection, and you should include as much information relevant to your academic ability and interests as you can. Examples are your A levels, your BSc dissertation, any publications (even in the form of a letter in newspaper), any experience as an editor (for example, for your school magazine). Your extracurricular activities are less important, and you can simply give a short list. At least one of the referees should be an academic - for example, your previous supervisor in your BSc degree.<br /> &nbsp;<br /> (3) Application to join a clinical course in another medical school Preclinical students who have completed an intercalated degree often have the option of applying to join a clinical course in another medical school, although it may become more difficult to do so with the introduction of the new GMC curriculum. Your CV is usually used for shortlisting candidates for interview. The criteria differ slightly among medical schools, but both academic ability and contribution to university life are important. Hence, not only should you highlight your academic achievements but you must also highlight your participation in the university (for example, in sports or music).&nbsp;<br /> <br /> (4) For the information of your tutor or counsellor For most medical schools, you are allocated a tutor who provides both academic and non-academic support and monitors your progress throughout your study on a confidential basis. Students are sometimes asked to submit their up to date CV to their tutors for information. Assuming that the tutors are helpful there is little to gain from over emphasising your strengths or hiding your weaknesses. Once you become a doctor in training after you qualify you will need to undergo an annual assessment of your progress. It serves to certify that you have reached a satisfactory standard, but it is also used as an aid to identify and help with your weaknesses. You may find it difficult to balance these two purposes in presenting your CV. General principles on presentation Now that all students are computer literate, there should be few problems in preparing a well presented CV. The following list serves as a reminder on how to present your CV effectively: Spelling or grammar mistakes - do not rely purely on the spell check on your computer. Ask friends to proofread your CV for you. Consistency - The use of punctuation to open and close sentences, justification, and fonts should be consistent. Readability - The headings should be clear. The font size should be no less than 12 point. Basic criteria - The basic criteria should be easily located, preferably on the first page. Length - The length of your CV increases as you progress up the professional ladder. For students, it should generally be no more than three pages. Quality of print - The CV should be printed on good quality paper, preferably using a laser printer. Practical points In this article, I argue that different versions of a CV may be required for different purposes. Even applications for different posts in the same specialty may require slightly different versions. Also, CVs need to be updated regularly. This would have been time consuming to achieve in the past, but it is now quite simple, with the aid of a basic word processing package. A master CV containing all relevant information should be prepared and saved as a computer file. This should be continuously kept up to date. When the need for a CV arises, it can be tailormade by editing the master document. It is important to save each of these edited versions separately, with the file names indicating the date when it was created and the purpose. It is also important to prepare a cover letter to go with the CV. Key messages A good CV is essential for successful progression up the medical professional ladder The contents of the CV should be tailormade for the purpose it is used for and the criteria against which it is judged. It is important to gather information about these criteria first The CV must be technically well presented, with the basic criteria easily located Information technology has made it simple to regularly update our CVs and allows preparation of different versions of a CV for different purposes with relative ease.</p><p><strong>Reference:</strong></p><p>Prepare a curriculum vitae. BMJ 1978;25(2):1478-9.<br /> O'Brien E. Prepare a curriculum vitae. In: Reece D, ed.&nbsp;<br /> How to do it. Vol 1. London: BMJ Publishing Group, 1995 Chambler AF, Chapman-Sheath PJ, Pearse MF.&nbsp;<br /> A model curriculum vitae: what are the trainers looking for? Hosp Med 1998;59(4):324-6.</p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/21365/a-guide-for-complete-r-beginners</guid>
	<pubDate>Fri, 20 Feb 2015 23:36:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/21365/a-guide-for-complete-r-beginners</link>
	<title><![CDATA[A guide for complete R beginners !]]></title>
	<description><![CDATA[<p>This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that &nbsp;biologists need to perform &nbsp;some basic analysis: &nbsp;load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).</p><p><em><span style="text-decoration: underline;">R-language: </span></em><a href="http://www.r-project.org/"><span style="color: #000080;"><span style="text-decoration: underline;"><em>http://www.</em></span></span><span style="color: #000080;"><span style="text-decoration: underline;"><em><strong>r</strong></em></span></span><span style="color: #000080;"><span style="text-decoration: underline;"><em>-project.org</em></span></span></a></p><p><em>BioConductor</em>:&nbsp;<a href="http://www.bioconductor.org/">http://www.bioconductor.org</a></p><p><strong>Advantages of R</strong></p><ul>
<li>Free!</li>
<li>Powerful, many libraries have been created to perform application specific tasks. e.g. analysis of microarray experiments and Next-Gen sequencing (bioconductor: including Bioseq group).</li>
<li>Presentation quality graphics
<ul>
<li>Save as a png, pdf or svg</li>
</ul>
</li>
<li>History
<ul>
<li>What you do can be saved for the next time you use R.</li>
<li>Ability to turn it into an automated script to perform again and again on different data</li>
</ul>
</li>
</ul><p><strong>Disadvantages</strong></p><ul>
<li>Lack of a comprehensive graphical user interface, but two do exist: However some do exist:&nbsp;R commander: <a href="http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/">http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/</a> and&nbsp;Limma-gui (microarrays) : <a href="http://bioinf.wehi.edu.au/limmaGUI/">http://bioinf.wehi.edu.au/limmaGUI/</a></li>
</ul><p><strong>Preparation</strong></p><ul>
<li>(Optional) Download and save the tutorial data set from
<ul>
<li>http://bioinformatics.knowledgeblog.org/wp-content/uploads/bioinf/kerr/data.tsv</li>
<li>Start R (type R on a Linux or Mac terminal, or find the starting link from PC)</li>
</ul>
</li>
</ul><p><strong>Getting More Help</strong></p><ul>
<li>Project Home page
<ul>
<li><span style="color: #000080;"><span style="text-decoration: underline;"><a href="http://www.r-project.org/">http://www.r-project.org/</a></span></span></li>
<li>Check out the &lsquo;introduction to R&rsquo;, which is a much more in depth guide .</li>
<li>Also R has a built-in help system (see later)</li>
</ul>
</li>
</ul><p><strong>Working directory</strong></p><p>This is the directory used to store your data and results. It is useful if it is also the directory where your input data is stored.</p><ul>
<li>Mac/Linux: this is the directory where you typed in R</li>
<li>PC: Change using the change working directory option</li>
</ul>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22133/r-320-is-released</guid>
	<pubDate>Sat, 18 Apr 2015 05:06:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22133/r-320-is-released</link>
	<title><![CDATA[R 3.2.0 is released]]></title>
	<description><![CDATA[<p>R 3.2.0 (codename &ldquo;Full of Ingredients&rdquo;)&nbsp;was <a href="http://r.789695.n4.nabble.com/R-3-2-0-is-released-td4705933.html" target="_blank">released yesterday</a>.&nbsp;You can get the latest binaries version <strong><a href="http://cran.rstudio.com/" target="_blank">from here</a>.</strong>&nbsp;(or the .tar.gz&nbsp;<strong>source</strong> code from <a href="http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz" target="_blank">here</a>).&nbsp;The full list of new features and bug fixes is provided below.</p><h3>Upgrading to R 3.2.0 on Windows</h3><p>If you are using <strong>Windows&nbsp;</strong>you can easily upgrade to the latest version of R using <a href="http://cran.r-project.org/web/packages/installr/" target="_blank">the installr package</a>. Simply run the following code:</p><div><table>
<tbody>
<tr id="p612572">
<td id="p61257code2">
<pre><span style="color: #228b22;"># installing/loading the latest installr package:</span>
<span style="color: #0000ff; font-weight: bold;">install.<span>packages</span></span><span style="color: #080;">(</span><span style="color: #ff0000;">"installr"</span><span style="color: #080;">)</span><span style="color: #080;">;</span> <span style="color: #0000ff; font-weight: bold;">library</span><span style="color: #080;">(</span>installr<span style="color: #080;">)</span> <span style="color: #228b22;">#load / install+load installr</span>
&nbsp;
updateR<span style="color: #080;">(</span><span style="color: #080;">)</span> <span style="color: #228b22;"># updating R.</span></pre>
</td>
</tr>
</tbody>
</table></div><p><span>Running &ldquo;updateR()&rdquo; will detect if there is a new R version available, and if so it will download+install it (etc.).</span></p><p><span><strong>If you are an R blogger yourself</strong> you are invited to <a href="http://www.r-bloggers.com/add-your-blog/">add your own R content feed to this site</a> (<strong>Non-English</strong> R bloggers should add themselves- <a href="http://www.r-bloggers.com/lang/add-your-blog">here</a>)</span></p><h4>NEW FEATURES</h4><ul>
<li><code>anyNA()</code> gains a <code>recursive</code> argument.</li>
<li>When <code>x</code> is missing and <code>names</code> is not false (including the default value), <code>Sys.getenv(x, names)</code> returns an object of class <code>"Dlist"</code> and hence prints tidily.</li>
<li>(Windows.) <code>shell()</code> no longer consults the environment variable <span>SHELL</span>: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). <span>R_SHELL</span>, the preferred way to select a non-default shell, can be used instead.</li>
<li>Some unusual arguments to <code>embedFonts()</code> can now be specified as character vectors, and the defaults have been changed accordingly.</li>
<li>Functions in the <code>Summary</code> group duplicate less. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15798" target="_blank">PR#15798</a>)</li>
<li>(Unix-alikes.) <code>system(cmd, input = )</code> now uses &lsquo;shell-execution-environment&rsquo; redirection, which will be more natural if <code>cmd</code> is not a single command (but requires a POSIX-compliant shell). (Wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15508" target="_blank">PR#15508</a>)</li>
<li><code>read.fwf()</code> and <code>read.DIF()</code> gain a <code>fileEncoding</code> argument, for convenience.</li>
<li>Graphics devices can add attributes to their description in <code>.Device</code> and <code>.Devices</code>. Several of those included with <strong>R</strong> use a <code>"filepath"</code> attribute.</li>
<li><code>pmatch()</code> uses hashing in more cases and so is faster at the expense of using more memory. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15697" target="_blank">PR#15697</a>)</li>
<li><code>pairs()</code> gains new arguments to select sets of variables to be plotted against each other.</li>
<li><code>file.info(, extra_cols = FALSE)</code> allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.</li>
<li>New function <code>dir.exists()</code> in package <span>base</span> to test efficiently whether one or more paths exist and are directories.</li>
<li><code>dput()</code> and friends gain new controls <span>hexNumeric</span> and <span>digits17</span> which output double and complex quantities as, respectively, binary fractions (exactly, see <code>sprintf("%a")</code>) and as decimals with up to 17 significant digits.</li>
<li><code>save()</code>, <code>saveRDS()</code> and <code>serialize()</code> now support <code>ascii = NA</code> which writes ASCII files using <code>sprintf("%a")</code> for double/complex quantities. This is read-compatible with <code>ascii = TRUE</code> but avoids binary-&gt;decimal-&gt;binary conversions with potential loss of precision. Unfortunately the Windows C runtime&rsquo;s lack of C99 compliance means that the format cannot be read correctly there in <strong>R</strong> before 3.1.2.</li>
<li>The default for <code>formatC(decimal.mark =)</code> has been changed to be <code>getOption("OutDec")</code>; this makes it more consistent with <code>format()</code> and suitable for use in print methods, e.g. those for classes <code>"density"</code>, <code>"ecdf"</code>, <code>"stepfun"</code> and <code>"summary.lm"</code>.
<p><code>getOption("OutDec")</code> is now consulted by the print method for class <code>"kmeans"</code>, by <code>cut()</code>, <code>dendrogram()</code>, <code>plot.ts()</code> and <code>quantile()</code> when constructing labels and for the report from<code>legend(trace = TRUE)</code>.</p>
<p>(In part, wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15819" target="_blank">PR#15819</a>.)</p>
</li>
<li><code>printNum()</code> and hence <code>format()</code> and <code>formatC()</code> give a warning if <code>big.mark</code> and <code>decimal.mark</code> are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).</li>
<li><code>merge()</code> can create a result which uses long vectors on 64-bit platforms.</li>
<li><code>dget()</code> gains a new argument <code>keep.source</code> which defaults to <code>FALSE</code> for speed (<code>dput()</code> and <code>dget()</code> are most often used for data objects where this can make <code>dget()</code> many times faster).</li>
<li>Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.</li>
<li>A number of macros have been added in the new &lsquo;<span>share/Rd</span>&rsquo; directory for use in package overview help pages, and <code>promptPackage()</code> now makes use of them.</li>
<li><code>tools::parse_Rd()</code> gains a new <code>permissive</code> argument which converts unrecognized macros into text. This is used by <code>utils:::format.bibentry</code> to allow LaTeX markup to be ignored.</li>
<li><code>options(OutDec =)</code> can now specify a multi-byte character, e.g., <code>options(OutDec = "u00b7")</code> in a UTF-8 locale.</li>
<li><code>is.recursive(x)</code> is no longer true when <code>x</code> is an external pointer, a weak reference or byte code; the first enables <code>all.equal(x, x)</code> when <code>x .</code></li>
<li><code>ls()</code> (aka <code>objects()</code>) and <code>as.list.environment()</code> gain a new argument <code>sorted</code>.</li>
<li>The <code>"source"</code> attribute (which has not been added to functions by <strong>R</strong> since before <strong>R</strong> version 2.14.0) is no longer treated as special.</li>
<li>Function <code>returnValue()</code> has been added to give <code>on.exit()</code> code access to a function&rsquo;s return value for debugging purposes.</li>
<li><code>crossprod(x, y)</code> allows more matrix coercions when <code>x</code> or <code>y</code> are vectors, now equalling <code>t(x) %*% y</code> in these cases (also reported by Radford Neal). Similarly, <code>tcrossprod(x,y)</code> and <code>%*%</code> work in more cases with vector arguments.</li>
<li>Utility function <code>dynGet()</code> useful for detecting cycles, aka infinite recursions.</li>
<li>The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.</li>
<li><code>apply(m, 2, identity)</code> is now the same as the matrix <code>m</code> when it has <em>named</em> row names.</li>
<li>A new function <code>debuggingState()</code> has been added, allowing to temporarily turn off debugging.</li>
<li><code>example()</code> gets a new optional argument <code>run.donttest</code> and <code>tools::Rd2ex()</code> a corresponding <code>commentDonttest</code>, with a default such that <code>example(..)</code> in help examples will run <code>donttest</code> code only if used interactively (a change in behaviour).</li>
<li><code>rbind.data.frame()</code> gains an optional argument <code>make.row.names</code>, for potential speedup.</li>
<li>New function <code>extSoftVersion()</code> to report on the versions of third-party software in use in this session. Currently reports versions of <code>zlib</code>, <code>bzlib</code>, the <code>liblzma</code> from <code>xz</code>, PCRE, ICU, TRE and the <code>iconv</code> implementation.
<p>A similar function <code>grSoftVersion()</code> in package <span>grDevices</span> reports on third-party graphics software.</p>
<p>Function <code>tcltk::tclVersion()</code> reports the Tcl/Tk version.</p>
</li>
<li>Calling <code>callGeneric()</code> without arguments now works with primitive generics to some extent.</li>
<li><code>vapply(x, FUN, FUN.VALUE)</code> is more efficient notably for large <code>length(FUN.VALUE)</code>; as extension of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16061" target="_blank">PR#16061</a>.</li>
<li><code>as.table()</code> now allows tables with one or more dimensions of length 0 (such as <code>as.table(integer())</code>).</li>
<li><code>names(x) now clears the names of call and <code>...</code> objects.</code></li>
<li><code>library()</code> will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.</li>
<li>A new <code>plot()</code> method for class <code>"raster"</code> has been added.</li>
<li>New <code>check_packages_in_dir_changes()</code> function in package <span>tools</span> for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.</li>
<li>Speed-up from Peter Haverty for <code>ls()</code> and <code>methods:::.requirePackage()</code> speeding up package loading. (<a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16133" target="_blank">PR#16133</a>)</li>
<li>New <code>get0()</code> function, combining <code>exists()</code> and <code>get()</code> in one call, for efficiency.</li>
<li><code>match.call()</code> gains an <code>envir</code> argument for specifying the environment from which to retrieve the <code>...</code> in the call, if any; this environment was wrong (or at least undesirable) when the<code>definition</code> argument was a function.</li>
<li><code>topenv()</code> has been made <code>.Internal()</code> for speedup, based on Peter Haverty&rsquo;s proposal in <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16140" target="_blank">PR#16140</a>.</li>
<li><code>getOption()</code> no longer calls <code>options()</code> in the main case.</li>
<li>Optional use of <code>libcurl</code> (version 7.28.0 from Oct 2012 or later) for Internet access:
<ul>
<li><code>capabilities("libcurl")</code> reports if this is available.</li>
<li><code>libcurlVersion()</code> reports the version in use, and other details of the <code>"libcurl"</code> build including which URL schemes it supports.</li>
<li><code>curlGetHeaders()</code> retrieves the headers for <code>http://</code>, <code>https://</code>, <code>ftp://</code> and <code>ftps://</code> URLs: analysis of these headers can provide insights into the &lsquo;existence&rsquo; of a URL (it might for example be permanently redirected) and is so used in <code>R CMD check --as-cran</code>.</li>
<li><code>download.file()</code> has a new optional method <code>"libcurl"</code> which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.</li>
<li><code>url()</code> has a new method <code>"libcurl"</code> which handles more URL schemes and follows redirections. The default method is controlled by a new option <code>url.method</code>, which applies also to the opening of URLs <em>via</em> <code>file()</code> (which happens implicitly in functions such as <code>read.table</code>.)</li>
<li>When <code>file()</code> or <code>url()</code> is invoked with a <code>https://</code> or <code>ftps://</code> URL which the current method cannot handle, it switches to a suitable method if one is available.</li>
</ul>
</li>
<li>(Windows.) The DLLs &lsquo;<span>internet.dll</span>&rsquo; and &lsquo;<span>internet2.dll</span>&rsquo; have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an <strong>R</strong>session.
<p>The Windows internet functions are still selected by flag <span>&ndash;internet2</span> or <code>setInternet2()</code>. This can be overridden for an <code>url()</code> connection <em>via</em> its new <code>method</code> argument.</p>
<p><code>download.file()</code> has new method <code>"wininet"</code>, selected as the default by <span>&ndash;internet2</span> or <code>setInternet2()</code>.</p>
</li>
<li><code>parent.env&lt;-</code> can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.</li>
<li>New function <code>isLoadedNamespace()</code> for readability and speed.</li>
<li><code>names(env)</code> now returns all the object names of an <code>environment</code> <code>env</code>, equivalently to <code>ls(env, all.names = TRUE, sorted = FALSE)</code> and also to the names of the corresponding list,<code>names(as.list(env, all.names = TRUE))</code>. Note that although <code>names()</code> returns a character vector, the names have no particular ordering.</li>
<li>The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.</li>
<li>New function <code>trimws()</code> for removing leading/trailing whitespace.</li>
<li><code>cbind()</code> and <code>rbind()</code> now consider S4 inheritance during S3 dispatch and also obey <code>deparse.level</code>.</li>
<li><code>cbind()</code> and <code>rbind()</code> will delegate recursively to <code>methods::cbind2</code> (<code>methods::rbind2</code>) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).</li>
<li>(Windows.) <code>download.file(quiet = FALSE)</code> now uses text rather than Windows progress bars in non-interactive use.</li>
<li>New function <code>hsearch_db()</code> in package <span>utils</span> for building and retrieving the help search database used by <code>help.search()</code>, along with functions for inspecting the concepts and keywords in the help search database.</li>
<li>New function <code>.getNamespaceInfo()</code>, a no-check version of <code>getNamespaceInfo()</code> mostly for internal speedups.</li>
<li>The help search system now takes <span>keyword</span> entries in Rd files which are not standard keywords (as given in &lsquo;<span>KEYWORDS</span>&rsquo; in the <strong>R</strong> documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.</li>
<li>New <code>lengths()</code> function for getting the lengths of all elements in a list.</li>
<li>New function <code>toTitleCase()</code> in package <span>tools</span>, tailored to package titles.</li>
<li>The matrix methods of <code>cbind()</code> and <code>rbind()</code> allow matrices as inputs which have <em>2^31</em> or more elements. (For <code>cbind()</code>, wish of <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16198" target="_blank">PR#16198</a>.)</li>
<li>The default method of <code>image()</code> has an explicit check for a numeric or logical matrix (which was always required).</li>
<li><code>URLencode()</code> will not by default encode further URLs which appear to be already encoded.</li>
<li><code>BIC(mod)</code> and <code>BIC(mod, mod2)</code> now give non-NA numbers for <code>arima()</code> fitted models, as <code>nobs(mod)</code> now gives the number of &ldquo;used&rdquo; observations for such models. This fixes <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16198" target="_blank">PR#16198</a>, quite differently than proposed there.</li>
<li>The <code>print()</code> methods for <code>"htest"</code>, <code>"pairwise.htest"</code> and <code>"power.htest"</code> objects now have a <code>digits</code> argument defaulting to (a function of) <code>getOption("digits")</code>, and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.</li>
<li>Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.</li>
<li>The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.</li>
<li><code>unzip()</code> will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16243" target="_blank">PR#16243</a>).</li>
<li><code>methods()</code> reports S4 in addition to S3 methods; output is simplified when the <code>class</code> argument is used. <code>.S3methods()</code> and <code>methods::.S4methods()</code> report S3 and S4 methods separately.</li>
<li>Higher order functions such as the <code>apply</code> functions and <code>Reduce()</code> now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves <a href="https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16093" target="_blank">PR#16093</a>.</li>
</ul><p>More at http://cran.rstudio.com/</p><p>Reference: http://www.r-bloggers.com/r-3-2-0-is-released-using-the-installr-package-to-upgrade-in-windows-os/</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/22410/nicolas-corradi-lab</guid>
  <pubDate>Tue, 26 May 2015 16:19:02 -0500</pubDate>
  <link></link>
  <title><![CDATA[Nicolas Corradi Lab]]></title>
  <description><![CDATA[
<p>The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.<br />To achieve this goal, our team combines the power of next generation DNA sequencing and  bioinformatics with molecular biology and experimental procedures.</p>

<p>Main research topics:<br />- Comparative and Population Genomics of Plant Symbionts<br />- Parasite Genome Evolution<br />- Experimental Evolution of Microbial Symbionts and Parasites<br />- Phylogenomics of Early Branching Fungi</p>

<p>More at http://corradilab.weebly.com/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl</guid>
	<pubDate>Tue, 09 Jun 2015 23:35:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl</link>
	<title><![CDATA[Rosalind Problem Solution with Perl]]></title>
	<description><![CDATA[<p>Rosalind is a platform for learning bioinformatics and programming through problem solving. <a href="http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track">Take a tour</a> to get the hang of how Rosalind works.</p><p>Bioinformatics Textbook Track</p><p>Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track</p><p>I will provide solution of all the Rosalind problem with Perl for community.</p><p>Check out the right sidebar for more links ...</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22793/sequencing-by-xpansion</guid>
	<pubDate>Wed, 17 Jun 2015 20:58:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22793/sequencing-by-xpansion</link>
	<title><![CDATA[Sequencing By Xpansion]]></title>
	<description><![CDATA[<p>Sequencing By Xpansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 1000X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.</p><p>http://www.stratosgenomics.com/stratos-genomics-technology</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</guid>
	<pubDate>Sun, 28 Jun 2015 07:46:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts</link>
	<title><![CDATA[BioScripts]]></title>
	<description><![CDATA[<p>You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks.</p>
<p>The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.</p>
<p>https://code.google.com/p/biowiki/</p>
<p>https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk</p>
<p>NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&amp;projectsearch=Search+projects</p>
<p>NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&amp;projectsearch=Search+projects</p><p>Address of the bookmark: <a href="https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search" rel="nofollow">https://code.google.com/hosting/search?q=bioinformatics&amp;sa=Search</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/22995/bioinformatics-phd-postdoc-job-rejection</guid>
	<pubDate>Thu, 02 Jul 2015 08:52:46 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/22995/bioinformatics-phd-postdoc-job-rejection</link>
	<title><![CDATA[Bioinformatics PhD / PostDoc / Job Rejection]]></title>
	<description><![CDATA[<div><p>While your PhD or PostDoc application, it is more common that you got rejected by many professors. Don't disappoint reply it calmly.</p><p><img src="http://bioinformaticsonline.com/mod/photo/rejected1.png" alt="image" style="border: 0px; border: 0px;"></p><p>In grad school, I shared a house with three Bioinformatics PhD students. One, when he applied to a particular professor, received a letter that said, essentially, "If you are applying because you want to enrich yourself, great. If you are applying because you want a job, you should know that you won't get one." I am trying to tell you this is because if you, with a good background in Bioinformatics, are passing up opportunities, you must be a strong candidate in many areas. Enrich yourself.<br /><br /> So, my suggestion is take a deep breath, forgot about all. Don&rsquo;t take it personally. It's been usual processes while hunting for a good lab and professor. Take is positive, I am not sure why they reject, but don't worry perhaps the lab don't deserve you. Always remember there are billions of reasons not to hire someone for projects, especially in a research sector.<br /><br /> My suggestion, please do not whine about how you were a great research candidate for the post, and you just can't understand why they were so stupid as to have rejected you! This feeling will not win you any points in research, community. Especially, when in todays socially connected era everyone is linked. Remember, a nice E-mail saying, "I really wished to working with you on this project and I hope we cross paths again," is all you need to send to the professor. Send a thank you note to the professor. Thank them for the time they spend to judge you. In the future, If you and the professor (of your dream) are attending a bioinformatics conference, invite him/her to lunch (please remember to pay the bill). In today evolving scientific ere, always remember to build your solid network in order to get a job of interest. Join all possible networking sites like LinkedIn, ResearchGate, Acamedia, FB for the same reason. You as a researcher always build a bridge with student/researcher/colleague/professor who have the research potential to lead in research and hire you. Just because you didn't get this project, doesn't mean there isn't another that will open up in couple of month.<br /><br /> Mostly, jobs that are hard to get are hard to get. Only you can decide if the continued sacrifices are worth the expected payout. If it is, keep on plowing. Build relationships. Attend conferences.</p><p>Image ref @ JaSonYa</p></div>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur</guid>
  <pubDate>Tue, 07 Jul 2015 23:12:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[BISR Jaipur]]></title>
  <description><![CDATA[
<p>The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:</p>

<p>    Bioinformatics supports to researchers<br />    Customized training in Bioinformatics for researchers and faculty members<br />    Support in Installing, implementing and maintaining software on computer.<br />    Create awareness for taking preventive measure against data security<br />    Organize workshops on thrust ares of Bioinformatics<br />    Research Training to students of Biotechnology and Bioinformatics </p>

<p>More at http://bioinfo.bisr.res.in/index.php</p>
]]></description>
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