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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29917?offset=990</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/5436/the-anatomy-of-successful-computational-biology-software</guid>
	<pubDate>Thu, 10 Oct 2013 11:53:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/5436/the-anatomy-of-successful-computational-biology-software</link>
	<title><![CDATA[The anatomy of successful computational biology software]]></title>
	<description><![CDATA[<p>Creators of software widely used in computational biology discuss the factors that contributed to their success</p><p><em>Nature Biotechnology</em><span>&nbsp;spoke with Altschul and several other originators of computational biology software programs widely used today (</span><a href="http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html#t1">Table 1</a><span>). The conversations explored what makes certain software tools successful, the unique challenges of developing them for biological research and how the field of computational biology, as a whole, can move research agendas forward. What follows is an edited compilation of interviews.</span></p><p>Detail @&nbsp;<a href="http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html">http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html</a></p><p>News Source @ Nature</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44497/graphpath-a-graph-attention-model-for-molecular-stratification-with-interpretability-based-on-the-pathway-pathway-interaction-network</guid>
	<pubDate>Wed, 27 Mar 2024 20:51:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44497/graphpath-a-graph-attention-model-for-molecular-stratification-with-interpretability-based-on-the-pathway-pathway-interaction-network</link>
	<title><![CDATA[GraphPath: A graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network]]></title>
	<description><![CDATA[<p><span>Achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. In this paper, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling.</span></p>
<p><span><img src="https://github.com/amazingma/GraphPath/raw/main/Figures/GraphPath.png" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/amazingma/GraphPath" rel="nofollow">https://github.com/amazingma/GraphPath</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5663/network-analysis-indian-statistical-institute</guid>
  <pubDate>Wed, 16 Oct 2013 08:06:50 -0500</pubDate>
  <link></link>
  <title><![CDATA[Network Analysis @ Indian Statistical Institute]]></title>
  <description><![CDATA[
<p>Indian Statistical Institute Kolkata invites applications for the following posts</p>

<p>2013 Oct Advertisement from Indian Statistical Institute</p>

<p>Post: Network Analysis</p>

<p>No. of Positions:  01</p>

<p>Educational Qualifications:</p>

<p>Candidate should have passed BE/B.Tech Or Equivalent in Computer Science / Electrical Engineering / Electronics / Information Technology / Bioinformatics / Biotechnology with throughout first Class<br />Experience:</p>

<p>(details of experience required)<br />Pay Scale: INR Rs.16000-20000/-P.M.</p>

<p>Walk-In-Interview : 22 Oct 2013 at 10:30 AM</p>

<p>Download Official Notification:<br />http://www.isical.ac.in/JobApplicationFiles/MIU_0310201311433700.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library</guid>
	<pubDate>Wed, 09 Jan 2019 11:00:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library</link>
	<title><![CDATA[visNetwork: an R package for network visualization, using vis.js javascript library]]></title>
	<description><![CDATA[<div id="introduction">
<p><strong>visNetwork</strong>&nbsp;is an R package for network visualization, using&nbsp;<strong>vis.js</strong>&nbsp;javascript library (<a href="http://visjs.org/">http://visjs.org/</a>). All remarks and bugs are welcome on github :&nbsp;<a href="https://github.com/datastorm-open/visNetwork">https://github.com/datastorm-open/visNetwork</a>.</p>
</div>
<div id="features">
<h2>Features</h2>
<p>Based on&nbsp;<a href="http://www.htmlwidgets.org/">htmlwidgets</a>, so :</p>
<ul>
<li>compatible with&nbsp;<a href="http://shiny.rstudio.com/">shiny</a>, R Markdown documents, and RStudio viewer</li>
</ul>
<p>The package proposes all the features available in&nbsp;<strong>vis.js</strong>&nbsp;API, and even more with special features for R :</p>
<ul>
<li>easy to use</li>
<li>custom shapes, styles, colors, sizes, &hellip;</li>
<li>works smooth on any modern browser for up to a few thousand nodes and edges</li>
<li>interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, &hellip;)</li>
<li>visualize&nbsp;<code>rpart</code>&nbsp;tree</li>
<li></li>
</ul>
</div><p>Address of the bookmark: <a href="https://datastorm-open.github.io/visNetwork/" rel="nofollow">https://datastorm-open.github.io/visNetwork/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5748/troyanskaya-lab</guid>
  <pubDate>Fri, 18 Oct 2013 10:57:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Troyanskaya  Lab]]></title>
  <description><![CDATA[
<p>In our research, we combine computational methods with an experimental component in a unified effort to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic disorders, such as cancer, and others whose failure might produce developmental defects in model systems.</p>

<p>Research Interest<br />Genomic Data Integration</p>

<p>Microarray Analysis</p>

<p>Gene and Protein Function Prediction</p>

<p>Detection and Analysis of Chromosomal Abnormalities and Functional Evolution</p>

<p>Integration of Computation and Experiments</p>

<p>Identification of Biological Networks and Pathways</p>

<p>Evaluation and Validation of Computational Predictions</p>

<p>Scalable Visualization-Based Data Analysis</p>

<p>More @ http://reducio.princeton.edu/cm/<br />PI page @ http://reducio.princeton.edu/cm/ogt</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps</guid>
	<pubDate>Mon, 10 Feb 2020 01:35:07 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps</link>
	<title><![CDATA[Leaflet: JavaScript libraries for interactive maps]]></title>
	<description><![CDATA[<p><a href="http://leafletjs.com/">Leaflet</a><span>&nbsp;is one of the most popular open-source JavaScript libraries for interactive maps.</span></p>
<h3>Features</h3>
<ul>
<li>Interactive panning/zooming</li>
<li>Compose maps using arbitrary combinations of:
<ul>
<li>Map tiles</li>
<li>Markers</li>
<li>Polygons</li>
<li>Lines</li>
<li>Popups</li>
<li>GeoJSON</li>
</ul>
</li>
<li>Create maps right from the R console or RStudio</li>
<li>Embed maps in&nbsp;<a href="http://yihui.name/knitr/">knitr</a>/<a href="http://rmarkdown.rstudio.com/">R Markdown</a>&nbsp;documents and&nbsp;<a href="http://shiny.rstudio.com/">Shiny</a>&nbsp;apps</li>
<li>Easily render spatial objects from the&nbsp;<code>sp</code>&nbsp;or&nbsp;<code>sf</code>&nbsp;packages, or data frames with latitude/longitude columns</li>
<li>Use map bounds and mouse events to drive Shiny logic</li>
<li>Display maps in non spherical mercator projections</li>
<li>Augment map features using chosen plugins from&nbsp;<a href="http://leafletjs.com/plugins">leaflet plugins repository</a></li>
</ul>
<p><a href="https://rstudio.github.io/leaflet/">https://rstudio.github.io/leaflet/</a></p><p>Address of the bookmark: <a href="https://rstudio.github.io/leaflet/" rel="nofollow">https://rstudio.github.io/leaflet/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5957/assistant-professor-in-molecular-synthesis-for-drug-discovery-and-development-cbmr-lucknow</guid>
  <pubDate>Wed, 30 Oct 2013 06:42:27 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor in Molecular Synthesis for Drug Discovery and Development @ CBMR, Lucknow]]></title>
  <description><![CDATA[
<p>ADVERTISEMENT FOR FACULTY POSITIONS AT CENTRE OF BIOMEDICAL RESEARCH (CBMR), LUCKNOW</p>

<p>Details of the Positions and Pay Structure:</p>

<p>03 Posts for Assistant Professor in Molecular Synthesis for Drug Discovery and Development</p>

<p>Essential Qualifications and Requirements:</p>

<p>1. PhD in Synthetic Organic Chemistry/Medicinal Chemistry with research publications in high quality international journals and first class grade at the preceding degree from recognised University/Institute in India or abroad with consistently good academic record.<br />2. Three Yrs of Post-doctoral experience in relevant area.<br />3. Below 35 Yrs of age at the time of application</p>

<p>Desirable Experience: Candidates having strong research background in organic synthesis, total synthesis of structurally complex and medicinally important natural products/drugs related to cancer, neurodegenerative diseases (neurotropically active molecules for Alzheimer's, Parkinson’s, dementia etc) and infectious diseases such as malaria, TB etc. will be preferred.</p>

<p>Interested candidates may apply with:</p>

<p>1. Filled up Application Form (download from CBMR Website: http://www.cbmr.res.in) along with the Cover Letter, Curriculum Vitae including academic record (Bachelor degree onwards), awards, honours, list of Publications and reprints of 5 best publications.<br />2. Proposed research plan (max 3-4 pages).<br />3. Names and address (with valid e-mail and Phone number) of at least 3 academic referees.<br />4. Online Payment Receipt with transaction reference no. of Rs. 1000/- (USD 100 or equivalent foreign currency) on following details.<br />Account Number: 30054847814 Name: Director, Centre of Biomedical Research<br />Bank: STATE BANK OF INDIA, SGPGI Campus Branch, LUCKNOW</p>

<p>IFSC Code: SBIN0007789<br />MICR No: 22602034</p>

<p>Applications can be sent by registered/speed post or by e-mail to the following address:</p>

<p>The Director,<br />Centre of Biomedical Research (CBMR),<br />Sanjay Gandhi PGI Campus,<br />Raebareli Road, Lucknow-226014<br />e-mail: cbmr.admin@cbmr.res.in,<br />gp.pandey@cbmr.res.in</p>

<p>More Info:</p>

<p>http://www.cbmr.res.in/career/Advertisement%20for%20the%20post%20of%20Professors%20and%20Assistant%20Professors.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35418/karyoploter-plot-whole-genomes-with-arbitrary-data</guid>
	<pubDate>Fri, 02 Feb 2018 03:24:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35418/karyoploter-plot-whole-genomes-with-arbitrary-data</link>
	<title><![CDATA[karyoploteR: plot whole genomes with arbitrary data]]></title>
	<description><![CDATA[<p><span><a href="http://bioconductor.org/packages/karyoploteR">karyoploteR</a></span><span>&nbsp;is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.</span></p><p>Address of the bookmark: <a href="https://bernatgel.github.io/karyoploter_tutorial/" rel="nofollow">https://bernatgel.github.io/karyoploter_tutorial/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24041/junior-bioinformatic-position</guid>
  <pubDate>Wed, 26 Aug 2015 05:35:28 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Bioinformatic position]]></title>
  <description><![CDATA[
<p>Junior Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:</p>

<p>We are seeking a highly motivated young PhD student with strong interest in high throughput data analysis.<br />Detailed descriptions of our recent research activities may be found here:<br />http://www.humanitas-research.org/condorelli-gianluigi-md-phd/</p>

<p>Position is available starting from October/November. A probationary period of one month will be required.<br /> <br />Please send a CV along with a cover letter stating the reasons for applying and contact details of one or more referees to Dr. Paolo Kunderfranco (paolo.kunderfranco@humanitasresearch.it).</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project</guid>
	<pubDate>Wed, 12 Dec 2018 08:33:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project</link>
	<title><![CDATA[genoPlotR - plot gene and genome maps project!]]></title>
	<description><![CDATA[<p>genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.</p>
<h3>Features</h3>
<ul>
<li>Linear representation of several segments of DNA</li>
<li>Comparisons represented by areas between the segments (like Artemis, for example)</li>
<li>Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files</li>
<li>Plot several subsegments of the same segment on the same line, separated by a //</li>
<li>Automatic or manual placement of the segments on the plot</li>
<li>Add annotations to all the lines</li>
<li>Create smart, automatic annotations for genomes, based on gene names</li>
<li>Add a user-generated tree</li>
<li>Add a global scale or a scale to each line</li>
<li>Use user-defined graphical functions to represent genes</li>
<li></li>
</ul><p>Address of the bookmark: <a href="http://genoplotr.r-forge.r-project.org/" rel="nofollow">http://genoplotr.r-forge.r-project.org/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

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