Difference between revisions of "Team:DTU-Denmark/Attributions"

 
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                     <div class="col-md-5 col-sm-5 hidden-xs intro"> <!-- will be hidden on phones, duplicate the text to blockquote down below first section header, to show it there, when it dissapear-->
 
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                             <p>“Silent gratitude isn't much use to anyone.</p>
                             <small>Someone famous in <cite title="Source Title">Source Title</cite></small>
+
                             <small><cite title="Source Title">Gladys B. Stern</cite></small>
 
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                 <p>“Silent gratitude isn't much use to anyone.</p>
                 <small>Someone famous in <cite title="Source Title">Source Title</cite></small>
+
                 <small>Gladys B. Stern<cite title="Source Title"></cite></small>
 
             </blockquote>
 
             </blockquote>
 
              
 
              
 
             <p>
 
             <p>
 
             <ul>
 
             <ul>
<li><b>Associate professor Mhairi Workman</b> helped us during our brainstorm phase with her great expertise in our organism <i> Yarrowia Lipolytica.</i></li>
+
<li><b>Associate professor Mhairi Workman</b> helped us during our brainstorm phase with her great expertise in our organism <i> Yarrowia lipolytica.</i></li>
 
<li><b>Professor Uffe Hasbro Mortensen</b> went through the design of our shuttle vector and generally helped us with the design of our molecular work.</li>
 
<li><b>Professor Uffe Hasbro Mortensen</b> went through the design of our shuttle vector and generally helped us with the design of our molecular work.</li>
<li><b> Head of Recruitment and Talent Development Malene Bonne Meyer</b> helped us with all aspects of budget and bureaucracy throughout the entire project.</li>
+
<li><b>Head of Recruitment and Talent Development Malene Bonne Meyer</b> helped us with all aspects of budget and bureaucracy throughout the entire project.</li>
<li><b>Graduate Student Researcher Cory Schwartz</b> and <b>Assistant professor Ian Wheeldon</b> kindly sent us our KU70 deficient <i> Yarrowia Lipolytica </i> strain. They also helped us with a transformation protocol and general tips for working with the organism. </li>
+
<li><b>Graduate Student Researcher Cory Schwartz</b> and <b>Assistant professor Ian Wheeldon</b> kindly sent us <i> Yarrowia lipolytica </i> PO1f and our <i>KU70</i> deficient <i> Y. lipolytica </i> PO1f strain. They also helped us with a transformation protocol and general tips for working with the organism, and supplied us with pIW357 and pIW501 that made it possible for us to knock out <i> PEX10 </i> and insert <i> URA3 </i> in the genome. </li>
<li><b>Ph.d student Patrice Lubuta</b> and <b>Ph.d student Anders Sebastian Rosenkrans Ødum</b> were present during our brainstorming sessions and gave us great inputs.</li>
+
<li><b>PhD student Patrice Lubuta</b> and <b>PhD student Anders Sebastian Rosenkrans Ødum</b> were present during our brainstorming sessions and gave us great inputs.</li>
 
<li><b>Pernille Neve Myers</b>, <b>Viktor Hesselberg-Thomsen</b> and <b>Vilhelm Krarup Møller</b> are all from last years team. They attended some of our general meetings helping us out with getting to know iGEM.</li>
 
<li><b>Pernille Neve Myers</b>, <b>Viktor Hesselberg-Thomsen</b> and <b>Vilhelm Krarup Møller</b> are all from last years team. They attended some of our general meetings helping us out with getting to know iGEM.</li>
  
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             <p>
 
             <p>
 
<ul>
 
<ul>
<li><b>Assistant professor Jakob Blæsbjerg Nielsen</b> provided our lab space and gave us great inputs on the use of CRISPR-Cas9. </li>
+
<li><b>Assistant professor Jakob Blæsbjerg Nielsen</b> provided us with a great laboratory space and gave us helpful input on the use of CRISPR-Cas9. </li>
<li><b>Postdoc Christina Spuur Nødvig</b> has been a great help during our daily work in the laboratory with her extensive knowledge about molecular work and CRISPR-Cas9. </li>
+
<li><b>Postdoc Christina Spuur Nødvig</b> has been a great help during our daily work in the laboratory with her extensive knowledge about molecular cloning and CRISPR-Cas9. </li>
<li><b>Postdoc Cristiano Varrano</b> ???</li>
+
<li><b>PhD student Ferdinand Hans Kirchner</b> has been a great help during our daily work in the laboratory with his extensive knowledge about molecular cloning and CRISPR-Cas9. </li>
<li><b>Laboratory Technician Louise</b> has provided help with navigating in the laboratory and has kindly produced the media we needed. </li>
+
<li><b>Postdoc Cristiano Varrano</b> for providing DAKA glycerine samples for substrate screening.</li>
<li><b>Benchling</b> is a great online tool that enabled us to have an online lab book that the entire team could access simultaneously. </li>
+
<li><b>Laboratory Intern Louise Svenningsen</b> and <b>Laboratory Technician Tina Johansen</b> have provided help with navigating in the laboratory and have kindly produced the media we needed. </li>
<li><b>Dansukker</b> ???</li></ul>
+
<li><b>Laboratory Technician Alexander Rosenkjær</b> patiently helped us use the Hamilton robot for substrate screening.</li>
 
+
<li><b>PhD student Peter Wolff</b> for help with RNA purification and rtPCR.</li>
 
+
<li><b>PhD student Malgorzata Ewa Futyma</b> provided great help with SDS page and transfer of SDS gels to nitrocellulose membranes.</li>
 
+
<li><b>PhD student Vinoth Wigneswaran</b> has provided help with OD- and fluorescence measurements during the Interlab study</li>
 +
<li><b>PhD student Anantha Vithakshana Peramuna</b> has provided help with fluorescent microscopy.</li>
 +
<li><b>Postdoc Sébastien Muller</b> provuded great help and consultancy during the western blotting efforts</li>
 +
<li><b>Food Technologist Preben Bøje Hansen</b> helped us with air compressor for extraction of substrate. </li>
 +
<li><b>Benchling</b>, which is a great online tool that enabled us to have an online lab book that the entire team could access simultaneously. </li>
 +
<li><b>Grønninggaard</b> kindly provided us with canola oil sediment for substrate screening and invited us out for a visit.</li>
 +
<li><b>Dansukker</b> kindly provided us with melasse for substrate screening.</li>
 +
<li><b>Perstorp HQ and Perstorp Bioproducts</b> kindly provided us with glycerine tech and crude samples for substrate screening.</li>
 +
<li><b>Emmelev A/S</b> kindly provided us with glycerine samples for substrate screening.</li>
 +
</ul>
 
             </p>
 
             </p>
 
         </div>
 
         </div>
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         <h2 class="h2">Modelling</h2>
 
         <h2 class="h2">Modelling</h2>
 
             <p>
 
             <p>
             Mikael Rørdam, Skylab, Chris Workman...?
+
<ul>
 +
             <li><b>Associate professor Mikael Rørdam Andersen</b> helped us with assessment of the initial strategy.</li>
 +
<li><b>Senior researcher Nikolaus Sonnenschein, PhD Anne Sofie Lærke Hansen and PhD Julian Brandl</b> guided us and helped us with troubleshooting and finding literature on Genome Scale Modeling of <i>Y. lipolytica</i>. </li>
 +
<li><b>PhD Kristian Jensen and PhD Joao Cardoso </b> helped us with model software setup and introduction. </li>
 +
<li><b>Benchling</b> is a great online tool that enabled us to have an online lab book that the entire team could access simultaneously. </li>
 +
<li><b>PhD student Patrice Lubuta</b> and <b>PhD student Anders Sebastian Rosenkrans Ødum</b> were great help with answering quesions about GSM, and providing and helping with experimental data for model validaiton. </li>
 +
<li><b>PhD Eduard Kerkhvoven</b> and <b>PhD Martin Kavsek</b> for helping us understand their GSM researches and answered many of our questions regarding thair papers</li>
 +
</ul>
 
             </p>
 
             </p>
  
 +
        </div>
 +
 +
        <div><a class="anchor" id="section-hard"></a>
 +
        <h2 class="h2">Hardware</h2>
 +
            <p>
 +
<ul>
 +
    <li><b>Associate professor Christopher Workman</b> came up with the idea of conducting automatic OD<sub>600</sub> measurements.</li>
 +
<li><b>Associate professor Martin Dufva</b> designed the very first measuring chamber.</li>
 +
<li><b>Docent Erik Vilain Thomsen</b> introduced us to electronics and suggested the light sensors, we used.</li>
 +
<li><b>Kennan Pinto from Biologigaragen</b> did user testing and came up with tons of ideas on how to improve the prototype.</li>
 +
<li>The <b>KiCad community</b> provided excellent documentation, tutorials and learning online.</li>
 +
<li><b>Oliver (user: SchrodingersGat)</b> provided templates for building shields for Arduino through GitHub.</li>
 +
<li>The <b>FreeCad community</b> provided excellent documentation, tutorials and learning online.</li>
 +
<li>The <b>Arduino community</b> provided excellent documentation, tutorials and learning online.</li>
 +
<li><b>DTU Skylab</b> provided resources for building and laser cutting.</li>
 +
</ul>
 +
<ul>
 +
<p> </p>
 +
<b>Authors of Arduino Libraries:</b>
 +
<li><b>Michael Margolis</b>, author of the DS1307RTC library.</li>
 +
<li>The author(s) of the TimeLib library (no credits are found in the files).</li>
 +
<li><b>DFRobot.com</b> and <b>Tim Starling</b>, authors of the LiquidCrystal_I2C library.</li>
 +
<li><b>Mark Stanley</b> and <b>Alexander Brevig</b>, authors of the Keypad library.</li>
 +
<li><b>Arduino.cc</b> provided the standard libraries: SD, SPI and Wire.</li>
 +
</ul>
 +
            </p>
 +
        </div>
 +
 +
        <div><a class="anchor" id="section-soft"></a>
 +
        <h2 class="h2">Software</h2>
 +
            <p>
 +
<ul>
 +
<li><b>Associate professor Christopher Workman</b> introduced the idea and importance of codon optimization to the team.</li>
 +
<li><b>Professor Mario dos Reis</b> published the tAI-based method that the optimization is based on.</li>
 +
<li><b>Python Software Foundation</b> provided Python.</li>
 +
</ul>
 
         </div>
 
         </div>
  
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<ul>
 
<ul>
 
<li><b>Pernille Neve Myers</b>, <b>Viktor Hesselberg-Thomsen</b> from the DTU iGEM team 2015 helped us during the BioBrick Tutorial. They were especially a great help in the laboratory work with BioBricks and also held a presentation with introduction to BioBrick assembly. </li>
 
<li><b>Pernille Neve Myers</b>, <b>Viktor Hesselberg-Thomsen</b> from the DTU iGEM team 2015 helped us during the BioBrick Tutorial. They were especially a great help in the laboratory work with BioBricks and also held a presentation with introduction to BioBrick assembly. </li>
<li><b>People from 301?!</b> (stefani)</li>
+
<li><b>Laboratory Technician Regina Åris Schürmann</b> has provided us with laboratory rooms and equipment for the BioBrick Tutorial.</li>
<li><b>Grønne Gården</b></li>
+
<li><b>Grønningaard</b></li>
 
+
<li><b> Novo Nordisk: Kjeld Olesen</b> and <b> Nina Gunnarson</b></li>
 
+
<li><b> Novozymes: Gernot J. Abel</b></li>
 +
<li><b>Mathias & Mathias - Tanken Bag Tale</b> helped us with presentation techniques.</li>
 +
<li><b>Biotech Academy</b> for collaboration on the Biosensor project. </li>
 
</ul>
 
</ul>
 
</div>
 
</div>
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<ul>
 
<ul>
<li><b>Mads Møller Madsen</b> from PF photo took pictures of the team.</li>
+
<li> <b>Mads Møller Madsen </b> from PF photo took pictures of the team.</li>
<li><b>Wiki Mads?</b></li>
+
<li><b>Mads Valdemar Anderson</b> gave advice on making the wiki.</li>
 
</div>
 
</div>
  
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   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>DTU</p>
+
       <p>The Technical University of Denamrk is a technical elite university with international reach and standards. Its mission is to develop and utilize natural and technical sciences to benefit society. The university houses 10,300 students and 5,800 employees focused on education, research, consultancy for the public sector and innovation, which contributes to increased growth and welfare - dtu.dk</p>
  
 
   </div>
 
   </div>
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   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>Blue dot</p>
+
       <p>Blue Dot is an initiative from DTU, where projects with a environmental focus are celebrated. Students work tegether across semesters, curricula and fields of study, students work with an engineering task that is greater than the individual study plan each semester, but is beneficial to society - dtu.dk</p>
  
 
   </div>
 
   </div>
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   <div class="col-md-6">
 
   <div class="col-md-6">
 
       <p>Lundbeckfonden is an active industrial foundation established in 1954. Its main objective is to maintain and expand the activities of the Lundbeck Group, and to provide funding for scientific research of the highest quality - lundbeckfonden.com</p>
 
       <p>Lundbeckfonden is an active industrial foundation established in 1954. Its main objective is to maintain and expand the activities of the Lundbeck Group, and to provide funding for scientific research of the highest quality - lundbeckfonden.com</p>
 
 
   </div>
 
   </div>
 
</div>
 
</div>
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<div class="row sponsor-row">
 
<div class="row sponsor-row">
 
   <div class="col-md-6">
 
   <div class="col-md-6">
     <img src="https://static.igem.org/mediawiki/2016/f/ff/DTU-Denmark--Otto_M%C3%B8nsted_fonden.png" class="sponsor-image">
+
     <img src="https://static.igem.org/mediawiki/2016/c/cf/T--DTU-Denmark--novozymes.png" class="sponsor-image">
 
   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>Otto Mønsted Fonden was founded in 1916. The fund supports and contributes to the Danish Trade and industry. They also supports research and educational science within the technical science and commercial disciplines. </p>
+
       <p>World leader in biological solutions. Novozymes produces a wide range of industrial enzymes and microorganisms, providing innovative answers to some of the world’s most pressing challenges - novozymes.com</p>
  
 +
  </div>
 +
</div>
 +
 +
 +
 +
 +
<div class="row sponsor-row">
 +
  <div class="col-md-6">
 +
    <img src="https://static.igem.org/mediawiki/2016/f/ff/DTU-Denmark--Otto_M%C3%B8nsted_fonden.png" class="sponsor-image">
 +
  </div>
 +
  <div class="col-md-6">
 +
      <p>Otto Mønsted Fonden was founded in 1916. The fund supports and contributes to the Danish Trade and industry. They also supports research and educational science within the technical science and commercial disciplines - www.omfonden.dk</p>
 
   </div>
 
   </div>
 
</div>
 
</div>
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   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>Bio Rad</p>
+
       <p>Bio-rad provides innovative and useful products that help life science researchers accelerate the discovery process and medical diagnostic labs obtain faster, better results - www.bio-rad.com</p>
  
 
   </div>
 
   </div>
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   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>Description of InVitro</p>
+
       <p>In Vitro is an exclusive distributor for a number of leading manufacturers from around the world, continuously specialising and introduce new products. The range covers equipment and consumables within Life science research. - in-vitro.dk</p>
  
 
   </div>
 
   </div>
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   </div>
 
   </div>
 
   <div class="col-md-6">
 
   <div class="col-md-6">
       <p>Description of Qiagen A/S</p>
+
       <p>Qiagen is a provider of sample and assay technologies for molecular diagnostics, applied testing, academic and pharmaceutical research - qiagen.com</p>
  
 
   </div>
 
   </div>
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             <li><a href="#section-1">Initial start-up phase</a></li>
 
             <li><a href="#section-1">Initial start-up phase</a></li>
 
             <li><a href="#section-2">Laboratory work</a></li>
 
             <li><a href="#section-2">Laboratory work</a></li>
             <li><a href="#section-3">Modelling</a></li>
+
             <li><a href="#section-3">Modeling</a></li>
 +
<li><a href="#section-hard">Hardware</a></li>
 +
<li><a href="#section-soft">Software</a></li>
 
             <li><a href="#section-4">Human practices</a></li>
 
             <li><a href="#section-4">Human practices</a></li>
 
             <li><a href="#section-5">Art & Design</a></li>
 
             <li><a href="#section-5">Art & Design</a></li>

Latest revision as of 01:35, 2 December 2016

New HTML template for the wiki




Bootstrap Example

Attributions

At the DTU BioBuilders team, we are lucky to be surrounded by very skilled people, who are willing to help us. A great thanks to everyone! Please note that all project work and otherwise presented activities on this wiki are performed by our team and high school students.


Initial Start-up Phase

“Silent gratitude isn't much use to anyone.”

Gladys B. Stern

  • Associate professor Mhairi Workman helped us during our brainstorm phase with her great expertise in our organism Yarrowia lipolytica.
  • Professor Uffe Hasbro Mortensen went through the design of our shuttle vector and generally helped us with the design of our molecular work.
  • Head of Recruitment and Talent Development Malene Bonne Meyer helped us with all aspects of budget and bureaucracy throughout the entire project.
  • Graduate Student Researcher Cory Schwartz and Assistant professor Ian Wheeldon kindly sent us Yarrowia lipolytica PO1f and our KU70 deficient Y. lipolytica PO1f strain. They also helped us with a transformation protocol and general tips for working with the organism, and supplied us with pIW357 and pIW501 that made it possible for us to knock out PEX10 and insert URA3 in the genome.
  • PhD student Patrice Lubuta and PhD student Anders Sebastian Rosenkrans Ødum were present during our brainstorming sessions and gave us great inputs.
  • Pernille Neve Myers, Viktor Hesselberg-Thomsen and Vilhelm Krarup Møller are all from last years team. They attended some of our general meetings helping us out with getting to know iGEM.

Laboratory Work

  • Assistant professor Jakob Blæsbjerg Nielsen provided us with a great laboratory space and gave us helpful input on the use of CRISPR-Cas9.
  • Postdoc Christina Spuur Nødvig has been a great help during our daily work in the laboratory with her extensive knowledge about molecular cloning and CRISPR-Cas9.
  • PhD student Ferdinand Hans Kirchner has been a great help during our daily work in the laboratory with his extensive knowledge about molecular cloning and CRISPR-Cas9.
  • Postdoc Cristiano Varrano for providing DAKA glycerine samples for substrate screening.
  • Laboratory Intern Louise Svenningsen and Laboratory Technician Tina Johansen have provided help with navigating in the laboratory and have kindly produced the media we needed.
  • Laboratory Technician Alexander Rosenkjær patiently helped us use the Hamilton robot for substrate screening.
  • PhD student Peter Wolff for help with RNA purification and rtPCR.
  • PhD student Malgorzata Ewa Futyma provided great help with SDS page and transfer of SDS gels to nitrocellulose membranes.
  • PhD student Vinoth Wigneswaran has provided help with OD- and fluorescence measurements during the Interlab study
  • PhD student Anantha Vithakshana Peramuna has provided help with fluorescent microscopy.
  • Postdoc Sébastien Muller provuded great help and consultancy during the western blotting efforts
  • Food Technologist Preben Bøje Hansen helped us with air compressor for extraction of substrate.
  • Benchling, which is a great online tool that enabled us to have an online lab book that the entire team could access simultaneously.
  • Grønninggaard kindly provided us with canola oil sediment for substrate screening and invited us out for a visit.
  • Dansukker kindly provided us with melasse for substrate screening.
  • Perstorp HQ and Perstorp Bioproducts kindly provided us with glycerine tech and crude samples for substrate screening.
  • Emmelev A/S kindly provided us with glycerine samples for substrate screening.

Modelling

  • Associate professor Mikael Rørdam Andersen helped us with assessment of the initial strategy.
  • Senior researcher Nikolaus Sonnenschein, PhD Anne Sofie Lærke Hansen and PhD Julian Brandl guided us and helped us with troubleshooting and finding literature on Genome Scale Modeling of Y. lipolytica.
  • PhD Kristian Jensen and PhD Joao Cardoso helped us with model software setup and introduction.
  • Benchling is a great online tool that enabled us to have an online lab book that the entire team could access simultaneously.
  • PhD student Patrice Lubuta and PhD student Anders Sebastian Rosenkrans Ødum were great help with answering quesions about GSM, and providing and helping with experimental data for model validaiton.
  • PhD Eduard Kerkhvoven and PhD Martin Kavsek for helping us understand their GSM researches and answered many of our questions regarding thair papers

Hardware

  • Associate professor Christopher Workman came up with the idea of conducting automatic OD600 measurements.
  • Associate professor Martin Dufva designed the very first measuring chamber.
  • Docent Erik Vilain Thomsen introduced us to electronics and suggested the light sensors, we used.
  • Kennan Pinto from Biologigaragen did user testing and came up with tons of ideas on how to improve the prototype.
  • The KiCad community provided excellent documentation, tutorials and learning online.
  • Oliver (user: SchrodingersGat) provided templates for building shields for Arduino through GitHub.
  • The FreeCad community provided excellent documentation, tutorials and learning online.
  • The Arduino community provided excellent documentation, tutorials and learning online.
  • DTU Skylab provided resources for building and laser cutting.

    Authors of Arduino Libraries:
  • Michael Margolis, author of the DS1307RTC library.
  • The author(s) of the TimeLib library (no credits are found in the files).
  • DFRobot.com and Tim Starling, authors of the LiquidCrystal_I2C library.
  • Mark Stanley and Alexander Brevig, authors of the Keypad library.
  • Arduino.cc provided the standard libraries: SD, SPI and Wire.

Software

  • Associate professor Christopher Workman introduced the idea and importance of codon optimization to the team.
  • Professor Mario dos Reis published the tAI-based method that the optimization is based on.
  • Python Software Foundation provided Python.

Human Practices

  • Pernille Neve Myers, Viktor Hesselberg-Thomsen from the DTU iGEM team 2015 helped us during the BioBrick Tutorial. They were especially a great help in the laboratory work with BioBricks and also held a presentation with introduction to BioBrick assembly.
  • Laboratory Technician Regina Åris Schürmann has provided us with laboratory rooms and equipment for the BioBrick Tutorial.
  • Grønningaard
  • Novo Nordisk: Kjeld Olesen and Nina Gunnarson
  • Novozymes: Gernot J. Abel
  • Mathias & Mathias - Tanken Bag Tale helped us with presentation techniques.
  • Biotech Academy for collaboration on the Biosensor project.

Art & Design

  • Mads Møller Madsen from PF photo took pictures of the team.
  • Mads Valdemar Anderson gave advice on making the wiki.

Funds

Sponsors

  • FIND US AT:
Facebook Twitter
  • DTU BIOBUILDERS
  • DENMARK
  • DTU - SØLTOFTS PLADS, BYGN. 221/002
  • 2800 KGS. LYNGBY

  • E-mail:
  • dtu-biobuilders-2016@googlegroups.com
  • MAIN SPONSORS:
Lundbeck fundation DTU blue dot Lundbeck fundation Lundbeck fundation