Difference between revisions of "Team:DTU-Denmark/Attributions"
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| − | <p> | + | <p>“Silent gratitude isn't much use to anyone.”</p> |
| − | <small> | + | <small><cite title="Source Title">Gladys B. Stern</cite></small> |
</blockquote> | </blockquote> | ||
</div> | </div> | ||
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<blockquote class="visible-xs"> <!-- quote from masterhead duplicate --> | <blockquote class="visible-xs"> <!-- quote from masterhead duplicate --> | ||
| − | <p> | + | <p>“Silent gratitude isn't much use to anyone.”</p> |
| − | <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 | + | <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> | + | <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>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>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> | ||
| Line 69: | Line 69: | ||
<p> | <p> | ||
<ul> | <ul> | ||
| − | <li><b>Assistant professor Jakob Blæsbjerg Nielsen</b> provided | + | <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>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>Postdoc Cristiano Varrano</b> for providing DAKA glycerine samples for substrate screening.</li> | <li><b>Postdoc Cristiano Varrano</b> for providing DAKA glycerine samples for substrate screening.</li> | ||
| − | <li><b>Laboratory | + | <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>Laboratory Technician Alexander Rosenkjær</b> patiently helped us use the Hamilton robot for substrate screening.</li> | <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 Peter Wolff</b> for help with RNA purification and rtPCR.</li> | ||
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<li><b>Postdoc Sébastien Muller</b> provuded great help and consultancy during the western blotting efforts</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>Food Technologist Preben Bøje Hansen</b> helped us with air compressor for extraction of substrate. </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>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>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>Dansukker</b> kindly provided us with melasse for substrate screening.</li> | ||
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<ul> | <ul> | ||
<li><b>Associate professor Mikael Rørdam Andersen</b> helped us with assessment of the initial strategy.</li> | <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 | + | <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 | + | <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>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> | </ul> | ||
</p> | </p> | ||
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</div> | </div> | ||
| − | <div><a class="anchor" id="section- | + | <div><a class="anchor" id="section-hard"></a> |
<h2 class="h2">Hardware</h2> | <h2 class="h2">Hardware</h2> | ||
<p> | <p> | ||
<ul> | <ul> | ||
| − | <li><b>Associate professor Christopher Workman</b> came up with the idea of conducting automatic | + | <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>Associate professor Martin Dufva</b> designed the very first measuring chamber.</li> | ||
| − | <li><b>Docent Erik Vilain Thomsen</b> introduced us to electronics and | + | <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><b>Kennan Pinto from Biologigaragen</b> did user testing and came up with tons of ideas on how to improve the prototype.</li> | ||
| − | <li><b>KiCad community</b> provided excellent documentation, tutorials and learning online.</li> | + | <li>The <b>KiCad community</b> provided excellent documentation, tutorials and learning online.</li> |
| − | <li><b>FreeCad 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><b>Arduino community</b> provided excellent documentation, tutorials and learning online.</li> | + | <li>The <b>FreeCad community</b> provided excellent documentation, tutorials and learning online.</li> |
| − | <li><b>DTU Skylab | + | <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> | </ul> | ||
</p> | </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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<li><b> Novo Nordisk: Kjeld Olesen</b> and <b> Nina Gunnarson</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> 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> | ||
| Line 138: | Line 160: | ||
<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>Mads Valdemar Anderson</b> gave advice on making the | + | <li><b>Mads Valdemar Anderson</b> gave advice on making the wiki.</li> |
</div> | </div> | ||
| Line 150: | Line 172: | ||
</div> | </div> | ||
<div class="col-md-6"> | <div class="col-md-6"> | ||
| − | <p>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> | + | <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> | ||
| Line 160: | Line 182: | ||
</div> | </div> | ||
<div class="col-md-6"> | <div class="col-md-6"> | ||
| − | <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 - | + | <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> | ||
| Line 184: | Line 206: | ||
</div> | </div> | ||
</div> | </div> | ||
| + | |||
| + | <div class="row sponsor-row"> | ||
| + | <div class="col-md-6"> | ||
| + | <img src="https://static.igem.org/mediawiki/2016/c/cf/T--DTU-Denmark--novozymes.png" class="sponsor-image"> | ||
| + | </div> | ||
| + | <div class="col-md-6"> | ||
| + | <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="row sponsor-row"> | ||
| Line 329: | Line 364: | ||
<li><a href="#section-3">Modeling</a></li> | <li><a href="#section-3">Modeling</a></li> | ||
<li><a href="#section-hard">Hardware</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
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.
- 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.
Authors of Arduino Libraries:
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
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
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
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
The Novo Nordisk Foundation uses its independence, flexibility and long-term perspective to promote world-class research. In this way the Foundation contributes to developing solutions that address the pressing challenges of the future – to benefit both individuals and society as a whole - novonordiskfonden.dk
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
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
Sponsors
Addgene, the nonprofit global plasmid repository, archives and distributes plasmids for scientists, while also providing free molecular biology resources - addgene.com
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
The BIONORDIKA GROUP was founded during 1986-1989. They offer a wide range of products and services focus in the areas of Cell & Molecular Biology, Immunology & Diagnostics, Instruments & Disposables and Custom Products & Projects - bionordika.dk
Eurofins Genomics is globally known for its innovative and customised technologies in the life science industries and academic research institutions. It is an international provider of DNA sequencing services, oligonucleotide synthesis products and bioinformatic services - eurofinsgenomics.eu
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
IDT specializes in DNA synthesis, gene construction, antisense oligos, molecular beacons and a variety of molecular biology products - idtdna.com
Mettler Toledo offers precisionsinstruments and services for many applications within research and decelopment, quality control, productions, logistics and retailing to customers worldwide - mt.com
New England Biolabs is a recognized world leader in the discovery, development and commercialization of recombinant and native enzymes for genomic research - neb.com
SnapGene offers the fastest and easiest way to plan, visualize, and document DNA cloning and PCR. You can easily annotate features and design primers - snapgene.com
VWR is a global supplier and distributor of labporatory equipement, chemicals, life science, consumables, equipments, instruments, furniture and service - vwr.com
Qiagen is a provider of sample and assay technologies for molecular diagnostics, applied testing, academic and pharmaceutical research - qiagen.com
