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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26309?offset=950</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material</guid>
	<pubDate>Sat, 18 Mar 2023 11:26:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material</link>
	<title><![CDATA[Bioinformatics Training Material !]]></title>
	<description><![CDATA[<p><span>Glittr</span>&nbsp;is a curated list of bioinformatics training material.<br>All material is:</p>
<ul>
<li>In a GitHub or GitLab repository</li>
<li>Free to use</li>
<li>Written in markdown or similar</li>
</ul>
<p><span>NOTE:</span>&nbsp;This list of courses is selected only based on the above criteria.<br>There are no checks on quality.</p>
<p>https://glittr.org/?per_page=25&amp;sort_by=stargazers&amp;sort_direction=desc</p><p>Address of the bookmark: <a href="https://glittr.org/?per_page=25&amp;sort_by=stargazers&amp;sort_direction=desc" rel="nofollow">https://glittr.org/?per_page=25&amp;sort_by=stargazers&amp;sort_direction=desc</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</guid>
	<pubDate>Tue, 18 Jun 2024 02:04:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</link>
	<title><![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]></title>
	<description><![CDATA[<p><span>BioKit is a set of tools dedicated to bioinformatics, data visualisation (</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.viz" title="biokit.viz"><code><span>biokit.viz</span></code></a><span>), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g.,&nbsp;</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.stats" title="biokit.stats"><code><span>biokit.stats</span></code></a><span>). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).</span></p><p>Address of the bookmark: <a href="https://biokit.readthedocs.io/en/latest/index.html" rel="nofollow">https://biokit.readthedocs.io/en/latest/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/853/ragan-lab</guid>
  <pubDate>Sun, 14 Jul 2013 12:03:43 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ragan Lab]]></title>
  <description><![CDATA[
<p>Computational systems biology</p>

<p>Research Area: <br />breast cancer; pancreatic cancer; prostate cancer; gastrointestinal disorders; urohaemolytic disorders; staphylococcal diseases</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/7989/cancers-cure-is-on-the-way</guid>
	<pubDate>Wed, 22 Jan 2014 12:00:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/7989/cancers-cure-is-on-the-way</link>
	<title><![CDATA[Cancers cure is on the way !!!]]></title>
	<description><![CDATA[<p>The study on blind mole rat (Spalax) was carried out by researchers from the University of Haifa, Israel, and published in the peer-reviewed scientific journal BMC Biology.</p><p>The blind mole rat (Spalax) is an intriguing creature worthy of study. This was animal research examining the resistance subterranean blind mole rats (Spalax) have to cancers. Blind mole rats are one of a unique group of animals that spend their lives underground, are tolerant of very low oxygen levels (down to only 3% concentration &ndash; levels that would kill a human), have a long lifespan of more than 20 years, which is exceptional for a small rodent, and show no clear signs of ageing or age-related diseases.</p><p>This research has demonstrated the unique abilities of the blind mole rat to resist cancer, even when directly given potent cancer-causing chemicals. In this study researchers gave blind mole rats potent cancer-causing chemicals either through injections or applied directly to the skin, but the animals didn't develop cancer.<br /><br />Remarkably, connective tissue cells (fibroblasts) taken from the blind mole rat even prevented the growth of human cancer cells when they were grown together in the laboratory.<br /><br />In the laboratory, the researchers also demonstrated how connective tissue cells called fibroblasts taken from the animal seem to play an important role in this cancer resistance. These cells prevented the growth of human cancer cells when the two types of cells were grown together in the laboratory.<br /><br />The researchers concluded that, "This report provides pioneering evidence that Spalax [the blind mole rat] is not only resistant to spontaneous cancer, but also to experimentally induced cancer, and shows the unique ability of Spalax fibroblasts to inhibit growth and kill cancer cells, but not normal cells, either through direct fibroblast-cancer cell interaction or via soluble factors."</p><p>Nonetheless, there remains optimism that understanding the anti-cancer mechanisms of mole rats may one day help inform further cancer treatments for humans, but a lot more research &ndash; and probably a significant amount of time &ndash; is needed before this can be considered.</p><p><img src="http://i.telegraph.co.uk/multimedia/archive/02599/naked-mole-rat_2599114b.jpg" alt="image" width="620" height="387" style="border: 0px; border: 0px;"></p><p>Reference:</p><p>Image: telegraph.co.uk</p><p>http://www.biomedcentral.com/1741-7007/11/91</p><p>Manov, Irena, et al. "Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: in vivo and in vitro evidence." BMC biology 11.1 (2013): 91.</p><p>http://www.nhs.uk/news/2014/01January/Pages/Claims-of-a-universal-cure-for-cancer-misleading.aspx</p><p>http://www.express.co.uk/news/health/454188/EXCLUSIVE-Cure-for-ALL-cancers-is-on-the-way-as-scientists-discover-major-breakthrough</p><p>http://www.dailymail.co.uk/health/article-2540321/Could-mole-rats-hold-key-cure-cancer-Scientists-hail-potentially-life-changing-breakthrough.html</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/38838/computer-scientistbioinformatician-at-ieo-in-milan-italy</guid>
  <pubDate>Thu, 31 Jan 2019 09:10:12 -0600</pubDate>
  <link></link>
  <title><![CDATA[Computer scientist/bioinformatician at IEO in Milan, Italy]]></title>
  <description><![CDATA[
<p>We are looking for a computer scientist or a bioinformatician with a strong computation background to join the bioinformatics unit of the IEO in Milan. Web development, scripting, experience with spring boot, hpc, docker are appreciated. The candidate will evolve in a research environment (next generation sequencing among others). The selected candidate will consolidate our team for the development and maintenance of the bioinformatics resources, and will have the opportunity to support the research groups in setting new tools and pipelines.</p>

<p>Place of employment and work</p>

<p>The candidate will be located at the Department of Experimental Oncology of the European Institute of Oncology in Milan (Italy), one of Europe’s leading research institutes in biomedical research, where he/she will also interact with one of the largest computational biology communities in Italy</p>

<p>Requirements:</p>

<p>The candidate should have a good knowledge of the UNIX system and good programming skills (bash, R, python, java). Background in bioinformatics would be appreciated but is not mandatory. Additional experience with containers (docker, singularity),  grid computing, web frameworks, continuous integrations will be appreciated.</p>

<p>For further info or to arrange an informal interview, please write to arnaud.ceol@ieo.it</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine</guid>
	<pubDate>Sat, 24 Aug 2013 15:47:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine</link>
	<title><![CDATA[Precision Medicine]]></title>
	<description><![CDATA[<p>Coupling established clinical&ndash;pathological indexes with state-of-the-art molecular profiling to create diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements &mdash; hence the term &ldquo;Precision medicine&rdquo;&nbsp;</p>
<p>Source:<a href="http://www.nejm.org/doi/full/10.1056/NEJMp1114866">http://www.nejm.org/doi/full/10.1056/NEJMp1114866</a></p>
<p><strong>Another video on precision medicine</strong>:</p>
<p><a href="http://www.youtube.com/watch?v=Pi8W0yOXnzE">http://www.youtube.com/watch?v=Pi8W0yOXnzE</a></p>
<p>Precision Medicine basically intergrates bioinformatics, genomics , genetics, molecular biology and nanotechnology to deliver precise cure/diagnotics to a specific patient.</p>
<p>Examples:</p>
<ul>
<li><span>The drug imatinib (Gleevec) designed to inhibit an altered enzyme produced by a fused version of two genes found in chronic myelogenous leukemia.</span></li>
<li><span>The breast cancer drug trastuzumab (Herceptin) works only for women whose tumors have a particular genetic profile called HER-2 positive.</span></li>
</ul>
<p><span>E.g. source :</span></p>
<p><span><a href="http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/">http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/</a></span></p><p>Address of the bookmark: <a href="http://www.cbsnews.com/video/watch/?id=50149783n" rel="nofollow">http://www.cbsnews.com/video/watch/?id=50149783n</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</guid>
	<pubDate>Thu, 12 Dec 2013 19:38:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</link>
	<title><![CDATA[Free math books]]></title>
	<description><![CDATA[<p>Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.</p>
<p>Please add ur links/bookmarks in comment section.</p><p>Address of the bookmark: <a href="http://physicsdatabase.com/free-math-books/" rel="nofollow">http://physicsdatabase.com/free-math-books/</a></p>]]></description>
	<dc:creator>Manisha Mishra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</guid>
	<pubDate>Mon, 28 May 2018 09:41:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</link>
	<title><![CDATA[Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.]]></title>
	<description><![CDATA[Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.<p>Address of the bookmark: <a href="https://github.com/Illumina/manta" rel="nofollow">https://github.com/Illumina/manta</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</guid>
	<pubDate>Sun, 22 Dec 2013 17:31:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</link>
	<title><![CDATA[Bioinformatics software for biologists in the genomics era]]></title>
	<description><![CDATA[<p>The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.</p><p>Address of the bookmark: <a href="http://bioinformatics.oxfordjournals.org/content/23/14/1713.full" rel="nofollow">http://bioinformatics.oxfordjournals.org/content/23/14/1713.full</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4725/complex-systems-from-physics-to-biology-october-15-16-2013-at-jnu-convention-center</guid>
  <pubDate>Mon, 23 Sep 2013 10:17:17 -0500</pubDate>
  <link></link>
  <title><![CDATA[Complex Systems: From Physics to Biology October 15-16 2013 at JNU Convention Center]]></title>
  <description><![CDATA[
<p>The symposium intents to focus on complex systems arising in a variety of settings in physics and biology. In particular, applications of the concepts of physics to biological sciences will be the major theme of this meeting.</p>

<p>Selected Topics:</p>

<p>    Cluster Dynamics<br />    Non-equilibrium Statistical Mechanics<br />    Forced Systems<br />    Hamiltonian Dynamics<br />    Synchronization &amp; Control<br />    Genomics &amp; Systems Biology<br />    Computational Neuroscience<br />    Econophysics</p>

<p>More @ http://www.jnu.ac.in/Conference/SCS2013/</p>
]]></description>
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