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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/14186?offset=20</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41041/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-mfd</guid>
  <pubDate>Sat, 15 Feb 2020 06:13:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[Post Doc Computational Biology, Bioinformatics - Network Biology &amp; Data Science, NGS (m/f/d)]]></title>
  <description><![CDATA[
<p>https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/forschung-entwicklung/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-129867.html?suid=e522e9793b41817e52ac58d6963b94e2519920df</p>

<p>Requirements<br />Doctoral degree in Bioinformatics, Computational Biology, (Bio)physics/-mathematics, Biochemistry/Biology or similar with strong quantitative and numeric focus<br />Ability to numerically process complex and large data sets<br />Good programming skills (R/Bioconductor and/or Python preferred, Linux is a plus)<br />Experience in analyzing next-generation sequencing data sets using network biology<br />Scientific publication record in applied bioinformatics<br />Familiarity with single cell NGS analyses and other –omics techniques is a plus, but not essential</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</guid>
	<pubDate>Fri, 23 Aug 2013 06:47:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</link>
	<title><![CDATA[Python and BioPython Tutorial]]></title>
	<description><![CDATA[<p>A quickstart tutorial that allows to become familiar with the Python language. The exercises expect knowledge of basic concepts of programming. A group of 2nd year computer science students with no previous Python knowledge required 60'-90' to complete the exercises. With about 3 hours time, the exercise is suitable for non-programmers as well.</p><p>Address of the bookmark: <a href="http://www.biotnet.org/training-materials/python-programmers" rel="nofollow">http://www.biotnet.org/training-materials/python-programmers</a></p>]]></description>
	<dc:creator>Manshi Raghubanshi</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory</guid>
  <pubDate>Wed, 18 Aug 2021 00:19:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at  Frederick National Laboratory]]></title>
  <description><![CDATA[
<p>Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR).  CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).</p>

<p>More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&amp;c=leidosbiomed&amp;id=2040</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</guid>
	<pubDate>Tue, 06 May 2014 01:10:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</link>
	<title><![CDATA[Check Linux server configuration !!]]></title>
	<description><![CDATA[<p>Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.<br /><br />To check what version of Operating System is installed on the server you can use the following commands:-<br />&nbsp;=================================================================<br />1.cat /etc/issue<br />[root@localhost ~]# cat /etc/issue<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Kernel \r on an \m<br /><br />2.cat /etc/redhat-release<br />[root@localhost ~]# cat /etc/redhat-release<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br /><br /><br />3.lsb_release -a<br />[root@localhost ~]# lsb_release -a<br />LSB Version:&nbsp;&nbsp;&nbsp; :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch<br />Distributor ID: RedHatEnterpriseServer<br />Description:&nbsp;&nbsp;&nbsp; Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Release:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.5<br />Codename:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Tikanga<br /><br /><br /><br />To check whether the operating system is 32 or 64bit:-<br />================================<br /># uname -i<br />[root@localhost ~]# uname -i<br />i386<br />(i386 represents that server is having 32bit operating system)<br /><br />[root@localhost ~]# uname -i<br />x86_64<br />(x86_64 represents that server is having 64bit operating system)<br /><br />To see the processor/CPU information:-<br />=============================<br /># cat /proc/cpuinfo<br />[root@localhost ~] cat /proc/cpuinfo<br />processor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />vendor_id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : GenuineIntel<br />cpu family&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />model&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 15<br />model name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : Intel(R) Xeon(R) CPU&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5130&nbsp; @ 2.00GHz<br />stepping&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />cpu MHz&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 1995.087<br />cache size&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 4096 KB<br />physical id&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />siblings&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />core id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />cpu cores&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />apicid&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />fdiv_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />hlt_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />f00f_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />coma_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />fpu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />fpu_exception&nbsp;&nbsp; : yes<br />cpuid level&nbsp;&nbsp;&nbsp;&nbsp; : 10<br />wp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />flags&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm<br />bogomips&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 3990.17<br />(Here processor number 0 indicates that the system is having one process(processor number starts with zero))<br /><br /><br /><br /><br />To check memory information:-<br />===========================<br /># free -m<br />[root@localhost ~]# free -m<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; total&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; used&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; free&nbsp;&nbsp;&nbsp;&nbsp; shared&nbsp;&nbsp;&nbsp; buffers&nbsp;&nbsp;&nbsp;&nbsp; cached<br />Mem:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5066&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3513&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1552&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 612&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2319<br />-/+ buffers/cache:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 582&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4484<br />Swap:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983<br /><br /><br /><br /># cat /proc/meminfo<br />[root@localhost ~]# cat /proc/meminfo<br />MemTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5187752 kB<br />MemFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1639300 kB<br />Buffers:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 627024 kB<br />Cached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2374944 kB<br />SwapCached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Active:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2458788 kB<br />Inactive:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 920964 kB<br />HighTotal:&nbsp;&nbsp;&nbsp;&nbsp; 4325164 kB<br />HighFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1561936 kB<br />LowTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 862588 kB<br />LowFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 77364 kB<br />SwapTotal:&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />SwapFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />Dirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 704 kB<br />Writeback:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />AnonPages:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 377892 kB<br />Mapped:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 35328 kB<br />Slab:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 153036 kB<br />PageTables:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6316 kB<br />NFS_Unstable:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Bounce:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />CommitLimit:&nbsp;&nbsp; 4625484 kB<br />Committed_AS:&nbsp;&nbsp; 977132 kB<br />VmallocTotal:&nbsp;&nbsp; 116728 kB<br />VmallocUsed:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4492 kB<br />VmallocChunk:&nbsp;&nbsp; 112124 kB<br />HugePages_Total:&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Free:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Rsvd:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />Hugepagesize:&nbsp;&nbsp;&nbsp;&nbsp; 2048 kB<br /><br /><br />To check the model and serial name of the server:-<br />=======================================<br />[root@localhost ~]#&nbsp; dmidecode | egrep -i "product name|Serial number"<br />Product Name: PowerEdge R710<br />Serial Number: AB8CDE1<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<br /><br />To check the host name:-<br />=====================<br />[root@localhost ~]# uname -n<br />localhost<br /><br />[root@localhost ~]# hostname<br />localhost<br /><br />To check the kernel version:-<br />========================<br />[root@localhost ~]# uname -r<br />2.6.18-238.9.1.el5PAE</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</guid>
	<pubDate>Mon, 24 Nov 2025 05:16:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</link>
	<title><![CDATA[Bioinformatics: The Bridge Between Curiosity and Discovery]]></title>
	<description><![CDATA[<p>In the sprawling universe of modern science, bioinformatics stands as one of the most transformative and empowering fields of our time. It is where biology meets computation, where data becomes meaning, and where curiosity becomes discovery. If you&rsquo;ve stepped into this world&mdash;or are considering it&mdash;here&rsquo;s your reminder: you&rsquo;re part of a revolution.</p><p><strong>Why Bioinformatics Matters More Than Ever</strong></p><p>Every day, our world generates massive amounts of biological data&mdash;from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.</p><p>Bioinformatics isn&rsquo;t just a skill.<br />It&rsquo;s the language of the future of biology.</p><p>By mastering it, you give yourself the power to:</p><p>Decode genomes and understand life at its most fundamental level</p><p>Identify patterns no microscope could ever reveal</p><p>Predict disease outbreaks before they occur</p><p>Accelerate drug discovery with computational precision</p><p>Contribute to open-source tools that empower scientists worldwide</p><p>You don&rsquo;t just follow science&mdash;you drive it.</p><p><strong>Every Expert Was Once a Beginner</strong></p><p>Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.</p><p>But here&rsquo;s the truth: every bioinformatician started exactly where you are now&mdash;curious, unsure, but excited.</p><p>No one writes perfect code on day one.</p><p>No one understands genomics pipelines immediately.</p><p>What makes you a bioinformatician is not perfection, but perseverance.</p><p>When your script throws a cryptic error&hellip;<br />When your data refuses to format&hellip;<br />When your pipeline runs for 6 hours only to crash&hellip;</p><p>Remember: this is part of the journey.<br />Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.</p><p>Bioinformatics Is Not Just a Career&mdash;It&rsquo;s a Mindset</p><p>It&rsquo;s the mindset of:</p><p>Problem-solving.</p><p>Continuous learning.</p><p>Turning chaos into clarity.</p><p>Seeing what others can&rsquo;t.</p><p>Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.</p><p><strong>Your Contribution Matters</strong></p><p>As you work on your script, pipeline, genome, or model, remember:</p><p>Somewhere, your analysis might contribute to:</p><p>A new therapy</p><p>A faster diagnostic test</p><p>A better understanding of a pathogen</p><p>A more resilient crop</p><p>An open-source dataset that helps thousands</p><p>A discovery that rewrites textbooks</p><p>Your code may be small, but its ripple effect is powerful.</p><p>The Future Is Bioinformatics&mdash;And You Are Part of It</p><p>The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.</p><p>This is a golden era&mdash;and you are not late.<br />You are exactly where you need to be.</p><p>Keep Pushing. Keep Learning. Keep Discovering.</p><p>Bioinformatics is a journey filled with challenges, but also with unmatched rewards.</p><p>So the next time you feel stuck, frustrated, or overwhelmed, remember:<br />You&rsquo;re building the science of tomorrow.</p><p>Be proud. Stay curious. Keep going.<br />Your work matters more than you think.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10460/assistant-professor-at-jawaharlal-nehru-university-in-delhi</guid>
  <pubDate>Wed, 07 May 2014 00:29:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor at Jawaharlal Nehru University in Delhi]]></title>
  <description><![CDATA[
<p>Advt. No. RC/48/2014</p>

<p>SCHOOL OF COMPUTATIONAL AND INTEGRATIVE SCIENCES (SC&amp;IS)</p>

<p>ESSENTIAL QUALIFICATION : - M.Sc./M.Tech. in Physics/ Chemistry/ Biology/ Mathematics/ Statistics/ Bioinformatics/ Computational Biology. Ph.D. in the broad areas of Bioinformatics/ Computational Biology. Candidates must have demonstrated capabilities in terms of high impact research publications in either of the above mentioned areas.</p>

<p>Scale of Pay : - 15600-39100/- (PB-III) AGP Rs. 6000/-</p>

<p>For more details on Centre/School, Specializations etc. please visit JNU website www.jnu.ac.in or contact Section Officer, Room Nos. 131-132, Recruitment Cell, Administrative Block, JNU, New Delhi – 110067, Email: recruitmentjnu2013@gmail.com The last date for the receipt of application is 15 May, 2014.</p>

<p>http://www.jnu.ac.in/Career/</p>

<p>http://www.jnu.ac.in/Career/ADVTNo_RC_48_2014.pdf<br />Last Apply Date:</p>

<p>15 May 2014</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy</guid>
	<pubDate>Mon, 07 May 2018 04:31:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy</link>
	<title><![CDATA[Installing  python-numpy !]]></title>
	<description><![CDATA[<p>$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose<br />[sudo] password for urbe: <br />Reading package lists... Done<br />Building dependency tree <br />Reading state information... Done<br />The following packages were automatically installed and are no longer required:<br /> bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic<br /> linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic<br /> linux-signed-image-4.4.0-116-generic runc ubuntu-fan<br />Use 'sudo apt autoremove' to remove them.<br />The following additional packages will be installed:<br /> blt fonts-lyx fonts-mathjax ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2 libhdf5-10 libjs-highlight<br /> libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4 python-chardet python-cvxopt<br /> python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging python-jdcal python-jinja2 python-joblib<br /> python-lxml python-markupsafe python-matplotlib-data python-mpmath python-numexpr python-openpyxl python-pandas-lib python-patsy python-pexpect<br /> python-pil python-ptyprocess python-py python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-simplegeneric<br /> python-simplejson python-statsmodels python-statsmodels-lib python-sympy-doc python-tables python-tables-data python-tables-lib python-tk<br /> python-tornado python-tz python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera<br />Suggested packages:<br /> blt-demo ipython-doc ipython-qtconsole python-pygments nodejs pandoc libiodbc2-dev libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info<br /> | gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras libjs-mathjax-doc python-gtk2-doc python-genshi python-jinja2-doc python-lxml-dbg<br /> python-lxml-doc ffmpeg inkscape python-cairocffi python-configobj python-excelerator python-matplotlib-doc python-qt4 python-sip python-traits<br /> python-wxgtk3.0 ttf-staypuft python-gmpy2 python-mpmath-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc python-pandas-doc<br /> python-patsy-doc python-pexpect-doc python-pil-doc python-pil-dbg subversion python-pytest-xdist libcurl4-gnutls-dev python-pycurl-dbg<br /> python-pycurl-doc python-pymysql-doc python-mock python-scipy-doc python-statsmodels-doc python-tables-doc python-netcdf vitables tix<br /> python-tk-dbg<br />The following NEW packages will be installed:<br /> blt fonts-lyx fonts-mathjax ipython ipython-notebook ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2<br /> libhdf5-10 libjs-highlight libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4<br /> python-chardet python-cvxopt python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging<br /> python-jdcal python-jinja2 python-joblib python-lxml python-markupsafe python-matplotlib python-matplotlib-data python-mpmath python-nose<br /> python-numexpr python-numpy python-openpyxl python-pandas python-pandas-lib python-patsy python-pexpect python-pil python-ptyprocess python-py<br /> python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-scipy python-simplegeneric python-simplejson python-statsmodels<br /> python-statsmodels-lib python-sympy python-sympy-doc python-tables python-tables-data python-tables-lib python-tk python-tornado python-tz<br /> python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera<br />0 upgraded, 73 newly installed, 0 to remove and 35 not upgraded.<br />Need to get 49,5 MB of archives.<br />After this operation, 271 MB of additional disk space will be used.<br />Do you want to continue? [Y/n] Y<br />Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pymysql all 0.7.2-1ubuntu1 [56,4 kB]<br />Get:2 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-3 [574 kB]<br />Get:3 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 blt amd64 2.5.3+dfsg-3 [4.852 B]<br />Get:4 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-lyx all 2.1.4-2 [161 kB]<br />Get:5 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-mathjax all 2.6.1-1 [960 kB]<br />Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-decorator all 4.0.6-1 [9.326 B]<br />Get:7 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-ptyprocess all 0.5-1 [12,9 kB]<br />Get:8 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pexpect all 4.0.1-1 [40,5 kB]<br />Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplegeneric all 0.8.1-1 [11,5 kB]<br />Get:10 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython all 2.4.1-1 [610 kB]<br />Get:11 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight.js all 8.2+ds-4build1 [151 kB]<br />Get:12 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight all 8.2+ds-4build1 [7.032 B]<br />Get:13 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-jquery-ui all 1.10.1+dfsg-1 [458 kB]<br />Get:14 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-marked all 0.3.2+dfsg-1 [12,7 kB]<br />Get:15 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-mathjax all 2.6.1-1 [5.601 kB]<br />Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libjs-underscore all 1.7.0~dfsg-1ubuntu1 [46,7 kB]<br />Get:17 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook-common all 2.4.1-1 [712 kB]<br />Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-markupsafe amd64 0.23-2build2 [15,5 kB]<br />Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-jinja2 all 2.8-1 [109 kB]<br />Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-pycurl amd64 7.43.0-1ubuntu1 [43,3 kB]<br />Get:21 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tornado amd64 4.2.1-1ubuntu3 [273 kB]<br />Get:22 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-zmq amd64 15.2.0-0ubuntu4 [200 kB]<br />Get:23 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook all 2.4.1-1 [48,4 kB]<br />Get:24 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 isympy all 0.7.6.1-1 [82,5 kB]<br />Get:25 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18,0 kB]<br />Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libamd2.4.1 amd64 1:4.4.6-1 [21,3 kB]<br />Get:27 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk36 amd64 4.57-1build3 [386 kB]<br />Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libgsl2 amd64 2.1+dfsg-2 [840 kB]<br />Get:29 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libsz2 amd64 0.3.2-1 [5.048 B]<br />Get:30 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-10 amd64 1.8.16+docs-4ubuntu1 [995 kB]<br />Get:31 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-antlr all 2.7.7+dfsg-6ubuntu1 [19,0 kB]<br />Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-bs4 all 4.4.1-1 [64,2 kB]<br />Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-chardet all 2.3.0-2 [96,3 kB]<br />Get:34 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libdsdp-5.8gf amd64 5.8-9.1ubuntu2 [192 kB]<br />Get:35 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cvxopt amd64 1.1.4-1.4 [1.344 kB]<br />Get:36 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cycler all 0.9.0-1 [5.426 B]<br />Get:37 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-dateutil all 2.4.2-1 [42,5 kB]<br />Get:38 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-glade2 amd64 2.24.0-4ubuntu1 [9.078 B]<br />Get:39 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-gmpy amd64 1.17-1 [91,1 kB]<br />Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-html5lib all 0.999-4 [83,1 kB]<br />Get:41 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pil amd64 3.1.2-0ubuntu1.1 [312 kB]<br />Get:42 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-imaging all 3.1.2-0ubuntu1.1 [4.596 B]<br />Get:43 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-jdcal all 1.0-1build1 [7.702 B]<br />Get:44 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-joblib all 0.9.4-1 [74,6 kB]<br />Get:45 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-lxml amd64 3.5.0-1build1 [819 kB]<br />Get:46 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB]<br />Get:47 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib-data all 1.5.1-1ubuntu1 [2.414 kB]<br />Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pyparsing all 2.0.3+dfsg1-1ubuntu0.1 [35,4 kB]<br />Get:49 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-tz all 2014.10~dfsg1-0ubuntu2 [31,5 kB]<br />Get:50 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-numpy amd64 1:1.11.0-1ubuntu1 [1.763 kB]<br />Get:51 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib amd64 1.5.1-1ubuntu1 [3.888 kB]<br />Get:52 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-mpmath all 0.19-3 [387 kB]<br />Get:53 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-nose all 1.3.7-1 [116 kB]<br />Get:54 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-numexpr amd64 2.4.3-1ubuntu1 [129 kB]<br />Get:55 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-openpyxl all 2.3.0-1 [193 kB]<br />Get:56 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas-lib amd64 0.17.1-3ubuntu2 [1.538 kB]<br />Get:57 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas all 0.17.1-3ubuntu2 [2.386 kB]<br />Get:58 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-patsy all 0.4.1-2 [169 kB]<br />Get:59 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-py all 1.4.31-1 [62,5 kB]<br />Get:60 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pyglet all 1.1.4.dfsg-3 [726 kB]<br />Get:61 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pytest all 2.8.7-4 [119 kB]<br />Get:62 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplejson amd64 3.8.1-1ubuntu2 [60,4 kB]<br />Get:63 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy all 0.7.6.1-1 [2.252 kB]<br />Get:64 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy-doc all 0.7.6.1-1 [4.774 kB]<br />Get:65 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-lib amd64 3.2.2-2 [353 kB]<br />Get:66 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-data all 3.2.2-2 [45,3 kB]<br />Get:67 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables all 3.2.2-2 [335 kB]<br />Get:68 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-tk amd64 2.7.12-1~16.04 [26,3 kB]<br />Get:69 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlrd all 0.9.4-1 [107 kB]<br />Get:70 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlwt all 0.7.5+debian1-1 [83,5 kB]<br />Get:71 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-scipy amd64 0.17.0-1 [8.733 kB]<br />Get:72 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels-lib amd64 0.6.1-4 [173 kB]<br />Get:73 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels all 0.6.1-4 [2.581 kB]<br />Fetched 49,5 MB in 0s (52,8 MB/s) <br />Extracting templates from packages: 100%<br />Selecting previously unselected package python-pymysql.<br />(Reading database ... 435155 files and directories currently installed.)<br />Preparing to unpack .../python-pymysql_0.7.2-1ubuntu1_all.deb ...<br />Unpacking python-pymysql (0.7.2-1ubuntu1) ...<br />Selecting previously unselected package tk8.6-blt2.5.<br />Preparing to unpack .../tk8.6-blt2.5_2.5.3+dfsg-3_amd64.deb ...<br />Unpacking tk8.6-blt2.5 (2.5.3+dfsg-3) ...<br />Selecting previously unselected package blt.<br />Preparing to unpack .../blt_2.5.3+dfsg-3_amd64.deb ...<br />Unpacking blt (2.5.3+dfsg-3) ...<br />Selecting previously unselected package fonts-lyx.<br />Preparing to unpack .../fonts-lyx_2.1.4-2_all.deb ...<br />Unpacking fonts-lyx (2.1.4-2) ...<br />Selecting previously unselected package 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/>Selecting previously unselected package python-tables.<br />Preparing to unpack .../python-tables_3.2.2-2_all.deb ...<br />Unpacking python-tables (3.2.2-2) ...<br />Selecting previously unselected package python-tk.<br />Preparing to unpack .../python-tk_2.7.12-1~16.04_amd64.deb ...<br />Unpacking python-tk (2.7.12-1~16.04) ...<br />Selecting previously unselected package python-xlrd.<br />Preparing to unpack .../python-xlrd_0.9.4-1_all.deb ...<br />Unpacking python-xlrd (0.9.4-1) ...<br />Selecting previously unselected package python-xlwt.<br />Preparing to unpack .../python-xlwt_0.7.5+debian1-1_all.deb ...<br />Unpacking python-xlwt (0.7.5+debian1-1) ...<br />Selecting previously unselected package python-scipy.<br />Preparing to unpack .../python-scipy_0.17.0-1_amd64.deb ...<br />Unpacking python-scipy (0.17.0-1) ...<br />Selecting previously unselected package python-statsmodels-lib.<br />Preparing to unpack .../python-statsmodels-lib_0.6.1-4_amd64.deb ...<br />Unpacking python-statsmodels-lib (0.6.1-4) ...<br />Selecting previously unselected package python-statsmodels.<br />Preparing to unpack .../python-statsmodels_0.6.1-4_all.deb ...<br />Unpacking python-statsmodels (0.6.1-4) ...<br />Processing triggers for libc-bin (2.23-0ubuntu10) ...<br />Processing triggers for fontconfig (2.11.94-0ubuntu1.1) ...<br />Processing triggers for man-db (2.7.5-1) ...<br />Processing triggers for hicolor-icon-theme (0.15-0ubuntu1) ...<br />Processing triggers for gnome-menus (3.13.3-6ubuntu3.1) ...<br />Processing triggers for desktop-file-utils (0.22-1ubuntu5.1) ...<br />Processing triggers for mime-support (3.59ubuntu1) ...<br />Processing triggers for doc-base (0.10.7) ...<br />Processing 5 added doc-base files...<br />Setting up python-pymysql (0.7.2-1ubuntu1) ...<br />Setting up tk8.6-blt2.5 (2.5.3+dfsg-3) ...<br />Setting up blt (2.5.3+dfsg-3) ...<br />Setting up fonts-lyx (2.1.4-2) ...<br />Setting up fonts-mathjax (2.6.1-1) ...<br />Setting up python-decorator (4.0.6-1) ...<br />Setting up python-ptyprocess (0.5-1) ...<br />Setting up python-pexpect (4.0.1-1) ...<br />Setting up python-simplegeneric (0.8.1-1) ...<br />Setting up ipython (2.4.1-1) ...<br />Setting up libjs-highlight.js (8.2+ds-4build1) ...<br />Setting up libjs-highlight (8.2+ds-4build1) ...<br />Setting up libjs-jquery-ui (1.10.1+dfsg-1) ...<br />Setting up libjs-marked (0.3.2+dfsg-1) ...<br />Setting up libjs-mathjax (2.6.1-1) ...<br />Setting up libjs-underscore (1.7.0~dfsg-1ubuntu1) ...<br />Setting up ipython-notebook-common (2.4.1-1) ...<br />Setting up python-markupsafe (0.23-2build2) ...<br />Setting up python-jinja2 (2.8-1) ...<br />Setting up python-pycurl (7.43.0-1ubuntu1) ...<br />Setting up python-tornado (4.2.1-1ubuntu3) ...<br />Setting up python-zmq (15.2.0-0ubuntu4) ...<br />Setting up ipython-notebook (2.4.1-1) ...<br />Setting up isympy (0.7.6.1-1) ...<br />Setting up libaec0:amd64 (0.3.2-1) ...<br />Setting up libamd2.4.1:amd64 (1:4.4.6-1) ...<br />Setting up libglpk36:amd64 (4.57-1build3) ...<br />Setting up libgsl2:amd64 (2.1+dfsg-2) ...<br />Setting up libsz2:amd64 (0.3.2-1) ...<br />Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...<br />Setting up python-antlr (2.7.7+dfsg-6ubuntu1) ...<br />Setting up python-bs4 (4.4.1-1) ...<br />Setting up python-chardet (2.3.0-2) ...<br />Setting up libdsdp-5.8gf (5.8-9.1ubuntu2) ...<br />Setting up python-cvxopt (1.1.4-1.4) ...<br />Setting up python-cycler (0.9.0-1) ...<br />Setting up python-dateutil (2.4.2-1) ...<br />Setting up python-glade2 (2.24.0-4ubuntu1) ...<br />Setting up python-gmpy (1.17-1) ...<br />Setting up python-html5lib (0.999-4) ...<br />Setting up python-pil:amd64 (3.1.2-0ubuntu1.1) ...<br />Setting up python-imaging (3.1.2-0ubuntu1.1) ...<br />Setting up python-jdcal (1.0-1build1) ...<br />Setting up python-joblib (0.9.4-1) ...<br />Setting up python-lxml (3.5.0-1build1) ...<br />Setting up ttf-bitstream-vera (1.10-8) ...<br />Setting up python-matplotlib-data (1.5.1-1ubuntu1) ...<br />Setting up python-pyparsing (2.0.3+dfsg1-1ubuntu0.1) ...<br />Setting up python-tz (2014.10~dfsg1-0ubuntu2) ...<br />Setting up python-numpy (1:1.11.0-1ubuntu1) ...<br />Setting up python-matplotlib (1.5.1-1ubuntu1) ...<br />Setting up python-mpmath (0.19-3) ...<br />Setting up python-nose (1.3.7-1) ...<br />Setting up python-numexpr (2.4.3-1ubuntu1) ...<br />Setting up python-openpyxl (2.3.0-1) ...<br />Setting up python-pandas-lib (0.17.1-3ubuntu2) ...<br />Setting up python-pandas (0.17.1-3ubuntu2) ...<br />Setting up python-patsy (0.4.1-2) ...<br />Setting up python-py (1.4.31-1) ...<br />Setting up python-pyglet (1.1.4.dfsg-3) ...<br />Setting up python-pytest (2.8.7-4) ...<br />Setting up python-simplejson (3.8.1-1ubuntu2) ...<br />Setting up python-sympy (0.7.6.1-1) ...<br />Setting up python-sympy-doc (0.7.6.1-1) ...<br />Setting up python-tables-lib (3.2.2-2) ...<br />Setting up python-tables-data (3.2.2-2) ...<br />Setting up python-tables (3.2.2-2) ...<br />Setting up python-tk (2.7.12-1~16.04) ...<br />Setting up python-xlrd (0.9.4-1) ...<br />Setting up python-xlwt (0.7.5+debian1-1) ...<br />Setting up python-scipy (0.17.0-1) ...<br />Setting up python-statsmodels-lib (0.6.1-4) ...<br />Setting up python-statsmodels (0.6.1-4) ...<br />Processing triggers for libc-bin (2.23-0ubuntu10) ...<br />➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1<br />Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=', mode 'w' at 0x7f85d1de31e0&gt;, longreads=[], mapq=10, mem=16, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)</p><p>##################################################<br />[Mon May 7 11:29:18 2018] Reduction...<br />#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]<br />/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.<br /> warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')<br />test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80</p><p>##################################################<br />[Mon May 7 11:29:29 2018] Estimating parameters of libraries...<br /> Aligning 19504 mates per library...<br />Insert size statistics Mates orientation stats<br />FastQ files read length median mean stdev FF FR RF RR<br />test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0<br />test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0</p><p>##################################################<br />[Mon May 7 11:29:29 2018] Scaffolding...<br /> iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603<br /> 19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].<br /> 1526 pairs. 558 in different contigs [36.57%].<br /> iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536<br /> 19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].<br /> 1077 pairs. 124 in different contigs [11.51%].<br /> iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536<br /> 19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].<br /> 3417 pairs. 396 in different contigs [11.59%].<br /> iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133<br /> 19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].<br /> 3398 pairs. 0 in different contigs [0.00%].</p><p>##################################################<br />[Mon May 7 11:29:34 2018] Gap closing...<br /> iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133</p><p>##################################################<br />[Mon May 7 11:29:35 2018] Final reduction...<br />#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]<br />[WARNING] Nothing reduced!<br />test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00</p><p>##################################################<br />[Mon May 7 11:29:35 2018] Reporting statistics...<br />#fname contigs bases GC [%] contigs &gt;1kb bases in contigs &gt;1kb N50 N90 Ns longest<br />test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603<br />test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603<br />test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603<br />test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536<br />test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536<br />test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133<br />test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133<br />test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133<br />test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390<br />test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390<br />test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390</p><p>##################################################<br />[Mon May 7 11:29:35 2018] Cleaning-up...<br />#Time elapsed: 0:00:17.376924</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/10749/memories-can-be-passed-down-through-dna</guid>
	<pubDate>Sat, 10 May 2014 21:24:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/10749/memories-can-be-passed-down-through-dna</link>
	<title><![CDATA[Memories Can Be Passed Down Through DNA]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/tbPwzII_g6o" frameborder="0" allowfullscreen></iframe>The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well.

Read More: 
Parental olfactory experience influences behavior and neural structure in subsequent generations
http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html
"Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood."

What Is Epigenetics?
http://www.sciencemag.org/content/330/6004/611
"The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics."

Epigenetics
http://en.wikipedia.org/wiki/Epigenetics

Watch More:
How to Change Your Genes
https://www.youtube.com/watch?v=B5DU9lgbsSE
TestTube Wild Card
http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC
Is Sexiness Hereditary?
https://www.youtube.com/watch?v=z6STRCncvM8
____________________

DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. 

Watch More DNews on TestTube http://testtube.com/dnews

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Discovery News http://discoverynews.com]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40214/gooey-turn-almost-any-python-command-line-program-into-a-full-gui-application-with-one-line</guid>
	<pubDate>Fri, 01 Nov 2019 00:29:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40214/gooey-turn-almost-any-python-command-line-program-into-a-full-gui-application-with-one-line</link>
	<title><![CDATA[Gooey: Turn (almost) any Python command line program into a full GUI application with one line]]></title>
	<description><![CDATA[<p><span>Turn (almost) any Python command line program into a full GUI application with one line</span></p>
<p>The easiest way to install Gooey is via&nbsp;<code>pip</code></p>
<pre><code>pip install Gooey 
</code></pre>
<p>Alternatively, you can install Gooey by cloning the project to your local directory</p>
<pre><code>git clone https://github.com/chriskiehl/Gooey.git
</code></pre>
<p>run&nbsp;<code>setup.py</code></p>
<pre><code>python setup.py install</code></pre><p>Address of the bookmark: <a href="https://github.com/chriskiehl/Gooey" rel="nofollow">https://github.com/chriskiehl/Gooey</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10773/bioinformatics-jrfsrf-position-at-national-research-centre-on-plant-biotechnology</guid>
  <pubDate>Sun, 11 May 2014 22:29:12 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/SRF position at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY]]></title>
  <description><![CDATA[
<p>NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY<br />LBS, CENTRE, PUSA CAMPUS, IARI NEW DELHI<br />NEW DELHI – 110 012</p>

<p>WALK- IN –INTERVIEWS</p>

<p>Eligible candidates may appear in Walk-in-Interview on May 23, 2014 at 10 AM for the posts of Research Associates &amp; Senior Research Fellows (SRF) in the following DST/DBT/ICAR funded projects.</p>

<p>1 NPTC Project on Bioinformatics and Comparative Genomics</p>

<p>Research Associate (One)</p>

<p>Rs. 24000/- + 30% HRA for masters degree holder with more than 4 years experience</p>

<p>Essential: Ph D in Plant Molecular Biology &amp; Biotechnology/Genetics 0r Candidates who have already submitted their Ph D thesis in above subjects</p>

<p>Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.</p>

<p>Senior Research Fellow ( UGCCSIR/ DBT/ ICAR Net qualified only): (One)</p>

<p>Rs. 16000/- + 30% HRA and Rs. 18000+30 HRA from 3rd year onwards</p>

<p>Essential:</p>

<p>1. ICAR/ UGCCSIR/DBT Net qualified only</p>

<p>2. M. Sc. (with thesis) in Biotechnology, Life Sciences, Biosciences/ Bioinformatics, Genetics/ Plant Pathology with experience in molecular biology.</p>

<p>Or M.Sc with more than 3 years research experiences</p>

<p>3. B.Sc. Agriculture or Biology</p>

<p>Desirable:<br />1. M. Sc. with thesis<br />2. Experience in molecular biology, plant tissue culture<br />3. Bioinformatics knowledge is important</p>

<p>2 DST JC Bose National Fellowship</p>

<p>Research Associate (Bioinformatics) : One</p>

<p>Rs.22000/- + 30% HRA for 1 &amp; 2nd Yr., Rs. 23000+ 30% HRA for 3rd year and Rs. 24000+30% HRA for 4th &amp;5th yr</p>

<p>Essential: M Ph D in Plant Molecular Biology &amp; Biotechnology/Genetics</p>

<p>Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.</p>

<p>Age limit: Max.35 years (Age relaxation of 5 years for SC/ST &amp; women and 3 years for OBC)</p>

<p>The posts are purely temporary in nature and are co-terminus with the project. Initially the offer will be made for one year only and may be further extendable based on performance of the candidate. The interview will be held on May 23 , 2014 at 10:00 AM at NRCPB, LBS Building, Pusa Campus, IARI, New Delhi- 110012. The candidates must bring four copies of biodata (in the prescribed proforma), original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph. No. TA/DA would be given for the appearance in interview. Only the candidates having essential qualification would be entertained for the interviews. Short-listing of candidates based on academic merit and experience will be done in case of large number of applicants.</p>

<p>Advertisement: http://www.nrcpb.org/sites/default/files/Advertisement%20for%20RA%20and%20SRF%20Position.pdf</p>
]]></description>
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