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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/38577?offset=190</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies</guid>
	<pubDate>Tue, 01 Jan 2019 11:56:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38561/hawkeye-an-interactive-visual-analytics-tool-for-genome-assemblies</link>
	<title><![CDATA[Hawkeye: an interactive visual analytics tool for genome assemblies]]></title>
	<description><![CDATA[<p><span>Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project&nbsp;</span><span><a href="http://amos.sourceforge.net/hawkeye"><span>http://amos.sourceforge.net/hawkeye</span></a></span><span>.</span></p>
<p>https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34</p><p>Address of the bookmark: <a href="http://amos.sourceforge.net/wiki/index.php?title=Hawkeye" rel="nofollow">http://amos.sourceforge.net/wiki/index.php?title=Hawkeye</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization</guid>
	<pubDate>Fri, 24 Jan 2020 04:09:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization</link>
	<title><![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]></title>
	<description><![CDATA[<p><span>MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from&nbsp;</span><code>https://github.com/linzhi2013/MitoZ</code><span>.</span></p>
<p><span><a href="https://academic.oup.com/nar/article/47/11/e63/5377471">https://academic.oup.com/nar/article/47/11/e63/5377471</a></span></p><p>Address of the bookmark: <a href="https://github.com/linzhi2013/MitoZ" rel="nofollow">https://github.com/linzhi2013/MitoZ</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44284/tools-for-geospatial-data-analysis</guid>
	<pubDate>Wed, 22 Mar 2023 02:10:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44284/tools-for-geospatial-data-analysis</link>
	<title><![CDATA[Tools for Geospatial data analysis !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data, and other forms of spatial data. They can help you visualize data, perform complex analysis, and even create maps and other visualizations.</p><p>The list includes some of the most popular and widely used geospatial tools available in Python. These tools can help you work with data from a variety of sources and in a variety of formats. Some of the tools are focused on visualization, such as Cartopy, Folium, and Contextily, which allow you to create interactive maps and other visualizations. Other tools are more focused on data manipulation and analysis, such as Fiona, GeoPandas, and Rasterio, which allow you to manipulate and analyze spatial data in a variety of ways.</p><p>The list also includes some tools for working with specific types of geospatial data. For example, the H3 library is designed specifically for working with hexagonal grids, while PySAL is focused on spatial econometrics and spatial analysis. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.</p><p>In summary, this list is an excellent resource for anyone working with geospatial data in Python. It contains a wide range of tools for working with different types of data, and can help you visualize data, perform complex analysis, and create maps and other visualizations. If you're looking to enhance your skills in geospatial analysis, this list is definitely worth checking out.</p></div></div></div><div><p>These tools are:</p><ul>
<li>ArcGIS - <a href="https://lnkd.in/dgC6sKJH" target="_new">https://lnkd.in/dgC6sKJH</a></li>
<li>Cartopy - <a href="https://lnkd.in/dc8ijXRg" target="_new">https://lnkd.in/dc8ijXRg</a></li>
<li>Contextily - <a href="https://lnkd.in/dTdQsmKX" target="_new">https://lnkd.in/dTdQsmKX</a></li>
<li>Descartes - <a href="https://lnkd.in/dCJykxwW" target="_new">https://lnkd.in/dCJykxwW</a></li>
<li>Fiona - <a href="https://lnkd.in/d8sJ3Q5a" target="_new">https://lnkd.in/d8sJ3Q5a</a></li>
<li>Folium - <a href="https://lnkd.in/dfSsE-MB" target="_new">https://lnkd.in/dfSsE-MB</a></li>
<li>GDAL - <a href="https://lnkd.in/dYBJBaAY" target="_new">https://lnkd.in/dYBJBaAY</a></li>
<li>Geohash - <a href="https://lnkd.in/d_NxJ4_M" target="_new">https://lnkd.in/d_NxJ4_M</a></li>
<li>GeoJSON - <a href="https://lnkd.in/daGs2WYq" target="_new">https://lnkd.in/daGs2WYq</a></li>
<li>GeoPandas - <a href="https://lnkd.in/dBTFKKV3" target="_new">https://lnkd.in/dBTFKKV3</a></li>
<li>Geopy - <a href="https://lnkd.in/dfAzR8Xa" target="_new">https://lnkd.in/dfAzR8Xa</a></li>
<li>Gevent - <a href="http://www.gevent.org/" target="_new">http://www.gevent.org</a></li>
<li>H3 - <a href="https://h3geo.org/docs/" target="_new">https://h3geo.org/docs/</a></li>
<li>OSMnx - <a href="https://lnkd.in/dm3pHgUS" target="_new">https://lnkd.in/dm3pHgUS</a></li>
<li>PyQGIS - <a href="https://lnkd.in/dShWyWVr" target="_new">https://lnkd.in/dShWyWVr</a></li>
<li>PySAL - <a href="https://pysal.org/" target="_new">https://pysal.org</a></li>
<li>Pydeck - <a href="https://lnkd.in/dGBFu-iw" target="_new">https://lnkd.in/dGBFu-iw</a></li>
<li>Pyproj - <a href="https://lnkd.in/dNG9fdkm" target="_new">https://lnkd.in/dNG9fdkm</a></li>
<li>RTree - <a href="https://lnkd.in/dURMiYpU" target="_new">https://lnkd.in/dURMiYpU</a></li>
<li>Rasterio - <a href="https://lnkd.in/dEMC6ve6" target="_new">https://lnkd.in/dEMC6ve6</a></li>
<li>Scikit-mobility - <a href="https://lnkd.in/dpHhaX2J" target="_new">https://lnkd.in/dpHhaX2J</a></li>
<li>Shapely - <a href="https://lnkd.in/d568datK" target="_new">https://lnkd.in/d568datK</a></li>
</ul><p>These tools offer a wide range of capabilities for working with geospatial data, from visualizing and manipulating data to performing complex analysis and modeling. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.</p></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44630/genofig-a-user-friendly-application-for-the-visualization-and-comparison-of-genomic-regions</guid>
	<pubDate>Mon, 05 Aug 2024 23:06:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44630/genofig-a-user-friendly-application-for-the-visualization-and-comparison-of-genomic-regions</link>
	<title><![CDATA[GenoFig: a user-friendly application for the visualization and comparison of genomic regions]]></title>
	<description><![CDATA[<p>Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [<a href="https://mjsull.github.io/Easyfig/" target="_blank">https://mjsull.github.io/Easyfig/</a>]</p>
<p dir="auto">Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:</p>
<div>
<pre id="code-47"><code><span>conda env create -f extras/requirements.yml</span>
<span>extras/SETUP.sh</span></code></pre>
</div><p>Address of the bookmark: <a href="https://forgemia.inra.fr/public-pgba/genofig" rel="nofollow">https://forgemia.inra.fr/public-pgba/genofig</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/view/119</guid>
	<pubDate>Wed, 10 Jul 2013 14:35:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/119</link>
	<title><![CDATA[Which are the best statistical programming languages to study for a bioinformatician?]]></title>
	<description><![CDATA[<p><span>In Bio-informatics based&nbsp;genome sequencing and predicting metabolic pathways&nbsp;research jobs&nbsp;I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.</span></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/857/smyth-lab</guid>
  <pubDate>Sun, 14 Jul 2013 12:26:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[Smyth Lab]]></title>
  <description><![CDATA[
<p>Statistical functional genomics in experimental medicine<br />The genome projects and the accelerated development of high-throughput genomic technologies such as microarrays have revolutionised biology. Making the most of this revolution requires the marriage of researchers from mathematical and biological backgrounds.</p>

<p>Research Area:<br />Linear models for microarray data<br />Digital gene expression technologies<br />Detection of molecular pathways<br />Bioinformatics resources for medical research</p>

<p>Link @ http://www.wehi.edu.au/faculty_members/professor_gordon_smyth/</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/914/welch-lab</guid>
  <pubDate>Mon, 15 Jul 2013 18:21:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Welch Lab]]></title>
  <description><![CDATA[
<p>They are based in the Department of Genetics at the University of Cambridge. </p>

<p>The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly evolutionary inference from genome sequence data.</p>

<p>Links @ http://www.gen.cam.ac.uk/research/welch/GroupPage/Home.html</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1466/iscb-asia-2013-translational-bioinformatics-conference</guid>
  <pubDate>Thu, 08 Aug 2013 06:31:32 -0500</pubDate>
  <link></link>
  <title><![CDATA[ISCB-Asia 2013 Translational Bioinformatics Conference]]></title>
  <description><![CDATA[
<p>ISCB-Asia 2013<br />Translational Bioinformatics Conference<br />Seoul, Korea<br />October 2 - 4, 2013</p>

<p>For more information visit: http://www.snubi.org/TBC2013/</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1491/2013-nextgen-genomics-bioinformatics-technologies-ngbt-conference-new-delhi-india</guid>
  <pubDate>Thu, 08 Aug 2013 16:21:16 -0500</pubDate>
  <link></link>
  <title><![CDATA[2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference, New Delhi, INDIA]]></title>
  <description><![CDATA[
<p>2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference</p>

<p>SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics &amp; Healthcare conference.</p>

<p>In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.</p>

<p>For more info : http://www.scigenomconferences.com/2013/default.php</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/1970/indias-own-first-drug-from-biocon</guid>
	<pubDate>Sun, 11 Aug 2013 16:05:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/1970/indias-own-first-drug-from-biocon</link>
	<title><![CDATA[India&#039;s own first drug - from Biocon.]]></title>
	<description><![CDATA[<p><span><span>Psoriasis is immune-mediated disease that effects the skin. the Disease on an average affects about 10-20 million Indians and it attacks the immune system of human beings. In generally occurs, when the immune system mistakes a normal skin cell for a pathogen, and sends out faulty signals that cause overproduction of new skin cells. <a href="http://en.wikipedia.org/wiki/Psoriasis">More at &gt;&gt;</a><br /></span></span></p><p><span><span>Biocon, India's largest publicly-held biotechnology firm, launched its second novel 'lab-to-market' molecule,<strong> Alzumab</strong>, to treat chronic plaque <strong>psoriasis</strong> at a cost 50 per cent lower than the existing one. </span></span></p><p><span><span><span><span>Biocon is bringing Alzumab (a biologic) in the form of a vial after working on it for nearly a decade. The work had initially started in a joint effort with the Center of Molecular Immunology, Havana, but Biocon took control of the programme soon after and also bought out its partner a few years ago. Biocon tell to the media that genotypic played a critical role in functional studies and clinical trial Genomics. </span></span><br /><br />The Biocon drug, at around&nbsp;₹ 7,500 a vial, will cost half as much as the currently available drugs - from Pfizer and J&amp;J - to treat psoriasis, a skin disease that causes rough red areas where the skin comes off in small pieces. A patient is usually prescribed to consume more than 40 vials in a 24-week course.<br /><br /></span></span></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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