User:Jarle Pahr

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*Jarle Pahr
*Jarle Pahr
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*Norwegian University of Science and Technology
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jarlemag@alumni.ntnu.no  
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jarlemag@stud.ntnu.no  
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*[[Special:Emailuser/Jarle Pahr|Email me through OpenWetWare]]
*[[Special:Emailuser/Jarle Pahr|Email me through OpenWetWare]]
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2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology
2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology
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==Research interests==
 
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<!-- Feel free to add brief descriptions to your research interests as well -->
 
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# Omega-3/poly-unsaturated fatty acid biosynthesis
 
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#Metabolic networks & Metabolic engineering
 
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# Molecular genetics of lactate utilization in bacteria
 
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#Bacterial stringent response
 
==Notes==
==Notes==
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[[User:Jarle Pahr/Algorithms|Algorithms]]
 
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[[User:Jarle Pahr/Applications|Apps]]
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See [[User:Jarle Pahr/Notes|Notes]]
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[[User:Jarle Pahr/16S_RNA|16S RNA]]
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[[User:Jarle Pahr/Biology|Biology]]
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[[User:Jarle Pahr/Bitesize|Bitesize Biology]]
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[[User:Jarle Pahr/BioBricks|BioBricks]]
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[[User:Jarle Pahr/Bioinformatics|Bioinformatics]]
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[[User:Jarpe Pahr/BAMBI|BAMBI]]
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[[User:Jarpe Pahr/BAMBI#BAMBI-LAST|BAMBI-LAST]]
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[[User:Jarpe Pahr/BAMBI#BAMBI-FAST|BAMBI-FAST]]
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[[User:Jarle Pahr/BLAST|BLAST]]
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[[User:Jarle Pahr/Books|Books]]
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[[User:Jarle Pahr/Buffers|Buffers]]
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[[User:Jarle Pahr/Calculations|Calculations]]
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[[User:Jarle Pahr/Checklists|Checklists]]
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[[User:Jarle Pahr/Chemicals|Chemicals]]
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[[User:Jarle Pahr/Cloning|Cloning]]
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[[User:Jarle Pahr/Computation|Computation]]
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[[User:Jarle Pahr/Control_theory|Control theory]]
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[[User:Jarle Pahr/Databases|Databases]]
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[[User:Jarle Pahr/DNA|DNA]]
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[[User:Jarle Pahr/Electrophoresis|Electrophoresis]]
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[[User:Jarle Pahr/Electronics|Electronics]]
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[[User:Jarle Pahr/Experiments|Experiments]]
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[[User:Jarle Pahr/Expression|Expression]]
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[[User:Jarle Pahr/Equipment|Equipment]]
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[[User:Jarle Pahr/Genes|Genes]]
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[[User:Jarle Pahr/Genetics|Genetics]]
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[[User:Jarle Pahr/Graph_theory|Graph theory]]
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[[User:Jarle Pahr/Growth_media|Growth media]]
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[[User:Jarle Pahr/Hardware|Hardware]]
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[[User:Jarle Pahr/iGEM|iGEM]]
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[[User:Jarle Pahr/lablessons|Lab lessons]]
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[[User:Jarle Pahr/Ligation|Ligation]]
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[[User:Jarle Pahr/Liquid_handling|Liquid handling]]
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[[User:Jarle Pahr/Microscopy|Microscopy]]
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[[User:Jarle Pahr/Models|Models]]
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[[User:Jarle Pahr/Microbiology|Microbiology]]
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[[User:Jarle Pahr/Organisms|Organisms]]
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[[User:Jarle Pahr/Oligonucleotides|Oligonucleotides]]
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[[User:Jarle Pahr/Simulations|Simulations]]
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[[User:Jarle Pahr/Open_science|Open science]]
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[[User:Jarle Pahr/Patents|Patents]]
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[[User:Jarle Pahr/Plasmids|Plasmids]]
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[[User:Jarle Pahr/Phylogenetics|Phylogenetics]]
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[[User:Jarle Pahr/Promoters|Promoters]]
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[[User:Jarle Pahr/Protocols|Protocols]]
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[[User:Jarle Pahr/PCR|PCR]]
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[[User:Jarle Pahr/Programming|Programming]]
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[[User:Jarle Pahr/Questions|Research questions]]
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[[User:Jarle Pahr/Recipes|Recipes]]
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[[User:Jarle Pahr/Restriction|Restriction]]
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[[User:Jarle Pahr/RNA|RNA]]
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[[User:Jarle Pahr/Safety|Safety]]
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[[User:Jarle Pahr/Software|Software]]
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[[User:Jarle Pahr/Statistics|Statistics]]
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[[User:Jarle Pahr/Sterilization|Sterilization]]
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[[User:Jarle Pahr/Synthetic_biology|Synthetic Biology]]
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[[User:Jarle Pahr/Systems_biology|Systems Biology]]
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[[User:Jarle Pahr/Transformation|Transformation]]
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[[User:Jarle Pahr/Vectors|Vectors]]
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[[User:Jarle Pahr/Vectors|Verification]]
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==Projects==
==Projects==
Line 149: Line 21:
==Organisms==
==Organisms==
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===Escherichia coli===
 
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===Mesoplasma florum===
 
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http://openwetware.org/wiki/Mesoplasma_florum
 
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http://partsregistry.org/Mesoplasma_florum
 
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http://microbewiki.kenyon.edu/index.php/Mesoplasma_florum
 
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http://www.broadinstitute.org/annotation/genome/mesoplasma_florum
 
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M. florum genome-scale model: http://biomodels.caltech.edu/BMID000000141045
 
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===Rhodococcus opacus===
 
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http://www.broadinstitute.org/blog/creature-feature-rhodococcus-opacus-pd630
 
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http://mic.sgmjournals.org/content/146/5/1143.full.pdf
 
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===B. subtilis===
 
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http://bsubcyc.org/
 
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===C. glutamicum===
 
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===Lactobacillus bulgaricus===
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See [[User:Jarle Pahr/Organisms|Organisms]]
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http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus
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==Interesting articles==
==Interesting articles==
Line 187: Line 36:
==Research centres/labs==
==Research centres/labs==
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Wyss institute: http://wyss.harvard.edu/
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Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/
Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/
Line 207: Line 59:
http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/
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http://korflab.ucdavis.edu/
==Research programs/projects==
==Research programs/projects==
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==Online learning==
==Online learning==
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'''Portals:'''
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See [[User:Jarle Pahr/Online_learning|Online learning]]
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http://www.class-central.com/
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http://www.core.org.cn
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https://www.coursera.org/
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MIT Open Courseware: http://ocw.mit.edu/index.htm
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https://www.udacity.com/
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https://www.edx.org/courses
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https://www.khanacademy.org
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'''Specific courses:'''
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Computational investing course: https://www.coursera.org/course/compinvesting1
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Linear and discrete optimization course: https://www.coursera.org/course/linearopt
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https://www.coursera.org/course/macroeconomics
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Bioinformatics algorithms: https://www.coursera.org/course/bioinformatics
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Financial Engineering: https://www.coursera.org/course/fe
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A beginner's guide to irrational behavior: https://www.coursera.org/course/behavioralecon
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Computational molecular evolution: https://www.coursera.org/course/molevol
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https://www.coursera.org/course/netsysbio
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Introduction to Systems Biology: https://www.coursera.org/course/sysbio
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==Language==
==Language==
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===Chinese===
 
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http://english.cntv.cn/learnchinese/
 
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http://popupchinese.com/
 
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http://www.sinosplice.com/
 
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http://www.clearchinese.com/learn-chinese
 
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http://www.instantspeakchinese.com/
 
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"The 5 stages of learning chinese:" http://www.sinosplice.com/learn-chinese/stages-to-learning-chinese
 
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Courses:
 
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http://www.languageinfusion.no/kinesiskonline.php?gclid=CNfCsP_N3LYCFc5a3godPh0ATQ
 
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http://www.learn-mandarin-help.com/software-to-learn-chinese.html
 
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http://www.rocketlanguages.com/chinese/premium/index.php?hop=jon1573
 
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http://chinesepod.com/
 
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http://www.sinosplice.com/learn-chinese/an-insiders-look-at-chinesepod
 
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http://store.instantimmersion.com/chinese.html
 
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http://www.fluenz.com/languages/mandarin/learn-mandarin/
 
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http://www.pimsleur.com/learn-mandarin-chinese
 
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http://www.learn-mandarin-help.com/rosetta-stone-mandarin.html
 
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http://www.amazon.com/Rosetta-Stone-Chinese-Mandarin-Level/dp/1608299643
 
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http://www.rosettastone.eu/lp/brand/?cid=se-ggeu1b13&rd=0
 
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http://www.learn-mandarin-help.com/
 
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http://www.fsi-language-courses.org/Content.php
 
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Foreign Service Institute language courses - Standard Chinese, a modular approach: http://www.fsi-language-courses.org/Content.php?page=Chinese
 
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http://ocw.mit.edu/courses/foreign-languages-and-literatures/21f-101-chinese-i-regular-spring-2006/
 
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Books:
 
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http://www.amazon.com/gp/product/7800521346/ref=cm_cr_asin_lnk
 
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New Practical Chinese Reader Textbook 1: http://www.amazon.com/New-Practical-Chinese-Reader-Textbook/dp/7561910401
 
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New Practical Chinese Reader series: http://www.sinoliterature.co.uk/english/index.aspx?category=68&gclid=CO2pyuLB3LYCFcNQ3god_CgAHg
 
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Reading/Writing:
 
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http://www.amazon.com/Reading-Writing-Chinese-Simplified-Character/dp/0804835098/ref=cm_cr-mr-title
 
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http://www.quickmandarin.com/chinesepinyintable/
 
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Dictionaries:
 
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http://www.nciku.com/
 
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http://www.zhongwen.com/
 
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Speaking:
 
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SpeakGoodChinese: http://www.speakgoodchinese.org/
 
==Synthetic Biology==
==Synthetic Biology==
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www.synthetic-bestiary.com
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See [[User:Jarle Pahr/Synthetic_biology|Synthetic Biology]]
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http://www.synbioproject.org/
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http://www.synbiont.org/
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Competitions and challenges:
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http://igem.org
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http://genocon.org/
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http://www.ia-sb.eu/go/synthetic-biology/
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LabGenius: www.labgeni.us
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http://synbio.org.uk/
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Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/
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Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html
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TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering: http://synthetic-biology.bbn.com/tasbe.html
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Raytheon BBN Synthetic biology publications: http://synthetic-biology.bbn.com/pubs.html'
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BBN Synthetic biology tools: https://synbiotools.bbn.com/
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http://www.synberc.org/
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http://www.teselagen.com/
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==Biological part collections==
==Biological part collections==
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https://registry.synberc.org/
https://registry.synberc.org/
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==DYI Bio/Citizen science==
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https://public-registry.jbei.org/ (http://www.ncbi.nlm.nih.gov/pubmed/22718978)
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http://bamh1.com/
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==DIY Bio/Citizen science==
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http://diyhpl.us/wiki/diybio/faq/
 
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http://www.lapaillasse.org
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See [[User:Jarle Pahr/DIYBio|DIY Bio]]
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http://openbioprojects.net/
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http://citizensciencequarterly.com/
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http://hackteria.org/
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==Art and Strategy==
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http://blogs.plos.org/citizensci/
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http://biocouture.co.uk/about/
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http://diybioftw.com/
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Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp
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http://dyibio.org
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http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment
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DYI Bio Europe: http://www.diybio.eu/
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http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/
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http://genefoo.com/
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http://blog.arduino.cc/2013/05/19/the-mood-lamp-recognizes-your-facial-expressions-and-turns-them-into-light/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer7d04e
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Open PCR: http://openpcr.org/
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http://thefinchandpea.com/2010/06/20/what-the-end-of-the-world-says-about-science/
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www.indiebiotech.com
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http://thefinchandpea.com/2013/08/04/sunday-poem-lord-byrons-post-apocalyptic-vision/
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Ask a Biosafety expert: http://ask.diybio.org/
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==Personal genomics==
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Public Laboratory: http://publiclaboratory.org/home
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https://www.23andme.com/
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BOSSLAB: http://bosslab.org/
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http://www.23andyou.com
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http://biocurious.org/
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http://www.genomesunzipped.org/
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http://genspace.org/
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uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
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Science hideout: http://www.youtube.com/user/ScienceHideout
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http://www.personalgenomes.org/
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http://basementbiotech.org/
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==Companies==
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http://www.biotinker.com/
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Evolutionary Solutions: http://www.evosol.co/
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BiologiGaragen: http://biologigaragen.org/
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http://www.allelebiotech.com/allele3/index.php
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http://haberlandt.blablablab.org/
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Era7: http://era7bioinformatics.com/en/index.cfm
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http://www.bugssonline.org/
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DNA electronics: http://dnae.co.uk/
-
Suggested Standard Operating Procedures for DYI Bio work: https://github.com/cathalgarvey/DIYbio-IE-SOPs
+
Genome Compiler: http://www.genomecompiler.com/
-
http://roningenetics.org/
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http://www.strandls.com
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https://www.biotinkering.org/
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http://www.novozymes.com/en/Pages/default.aspx
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http://www.genabler.com
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===Crowdfunding===
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http://www.kickstarter.com/
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https://www.microryza.com/
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http://www.indiegogo.com/
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http://www.gofundme.com/
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Projects:
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http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit
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http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
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===Contract research services===
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https://www.scienceexchange.com/
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===Home experiments/projects===
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-
(Legality may vary depending on your location)
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-
How to do a pGlo transformation: http://www.youtube.com/watch?v=sovDqqhQJx8
+
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-
http://www.instructables.com/id/The-Light-Fountain-a-Bioluminescent-Hourglass/
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-
http://cibt.bio.cornell.edu/workshops_and_summer_programs/0608alum/lumos.pdf
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-
http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/%3Eprotocol
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==Art and Strategy==
+
-
 
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-
Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp
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-
 
+
-
http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment
+
-
 
+
-
http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/
+
-
 
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-
==Personal genomics==
+
-
 
+
-
https://www.23andme.com/
+
-
 
+
-
http://www.23andyou.com
+
-
 
+
-
http://www.genomesunzipped.org/
+
-
 
+
-
uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome
+
-
 
+
-
http://www.personalgenomes.org/
+
-
 
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-
==Companies==
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http://www.syntheticgenomics.com/
http://www.syntheticgenomics.com/
Line 511: Line 170:
==Suppliers==
==Suppliers==
 +
 +
http://store.p212121.com/
 +
 +
http://www.biosciencetools.com/
 +
 +
http://www.laboratory-journal.com/
 +
 +
www.labx.com
 +
 +
http://www.oxfordgenetics.co.uk/
 +
 +
BioBasic: http://store.biobasic.com/
Promega: http://no.promega.com/
Promega: http://no.promega.com/
Line 551: Line 222:
http://www.sbsbio.com/english/dnahc.html
http://www.sbsbio.com/english/dnahc.html
 +
 +
http://www.interfarm.no/produkter/
http://www.iorodeo.com/
http://www.iorodeo.com/
 +
 +
'''Used equipment vendors:'''
 +
 +
http://www.labrecyclers.com/index.html
==Useful links==
==Useful links==
Line 559: Line 236:
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===Conferences===
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===Conferences and meetings===
-
SBx.0: http://sb6.biobricks.org/
 
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Advances in Genome Biology and Technology: http://agbt.org/about.html
 
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See [[User:Jarle Pahr/Conferences|Conferences]]
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Personal Genomes & Medical Genomics (PGMG) (Cold Spring Harbor Laboratories meeting).
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-
Biology of Genomes (BOG): https://meetings.cshl.edu/meetings/2013/genome13.shtml
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Beyond the Genome: http://www.beyond-the-genome.com/
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===Scientific challenges and competitions===
===Scientific challenges and competitions===
Line 582: Line 251:
Alignathon
Alignathon
 +
 +
Sequence squeeze: http://www.sequencesqueeze.org/
 +
 +
===Resources for researchers===
 +
 +
http://www.protocol-online.org/science-forums-2/Dissertation-and-Paper-Writing/
 +
 +
http://www.protocol-online.org/science-forums-2/Career-Advice/
 +
 +
https://www.researchgate.net
 +
 +
http://friendfeed.com/the-life-scientists
 +
 +
http://nigerianbioscientist.com/
===Educational resources===
===Educational resources===
Line 594: Line 277:
https://www.manylabs.org/
https://www.manylabs.org/
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http://www.dnalabbook.co.uk/
=Wiki sites=
=Wiki sites=
Line 604: Line 288:
http://ecoliwiki.net
http://ecoliwiki.net
 +
 +
http://www.phylocommons.org/
===Discussion and communities===
===Discussion and communities===
-
http://molecularbiology.forums.biotechniques.com/
+
===Apps===
-
DYI Bio Google Group: https://groups.google.com/forum/?fromgroups#!forum/diybio
+
mPartsregistry: http://mpartsregistry.appspot.com
-
http://www.americanbiotechnologist.com/blog/
+
===Persons/Research groups===
-
BioStar - questions and answers on bioinformatics and genomics: http://www.biostars.org/
+
http://genefish.wikispaces.com/
-
Biology.stackexchange.com: http://biology.stackexchange.com/
+
Mark Pallen: http://www2.warwick.ac.uk/fac/med/research/microinfect/staff/pallengroup/
-
http://www.biology-online.org/
+
Chris Anderson lab: https://andersonlab.qb3.berkeley.edu/
-
https://www.researchgate.net/
+
Magni Paolo: http://www.labmedinfo.org/people/magni
-
https://www.researchgate.net/topics/?nav=discussions
+
http://www.rpgroup.caltech.edu/publications/
-
http://www.protocol-online.org/biology-forums/
+
Heng Li. "Alignment God".  
-
Nature Protocols discussion forum: http://network.nature.com/groups/natureprotocols/forum/topics
+
Dworkin lab: https://www.msu.edu/~idworkin/publications.html
-
http://www.reddit.com/r/labrats/
+
Titus Brown:  
-
http://scienceboard.net/forum/default.asp
+
Erlich lab: http://erlichlab.wi.mit.edu/index.html
-
http://branch.com/g/level-headed-biotech
+
Cristopher mason: http://www.masonlab.net/
-
http://www.bio.net/
+
http://openwetware.org/wiki/User:Vincent
-
===Apps===
+
Markus Gershater
-
mPartsregistry: http://mpartsregistry.appspot.com
+
http://www.princeton.edu/~ajlgroup/
-
===Persons/Research groups===
+
Heng Li
 +
 
 +
Michael Cashel: https://science.nichd.nih.gov/confluence/display/pgd/Michael+Cashel+Lab
Jim Collins: http://www.bu.edu/abl/
Jim Collins: http://www.bu.edu/abl/
Line 653: Line 341:
Chris Voigt
Chris Voigt
-
Pallsson  
+
Bernahrd Ø Pallsson: http://gcrg.ucsd.edu/Researchers/Palsson
Tom Knight
Tom Knight
Line 675: Line 363:
Rob Carlson
Rob Carlson
 +
 +
Ethan Perlstein: http://www.perlsteinlab.com/
 +
 +
Anthony Evans
 +
 +
Nick Loman:
 +
 +
http://pathogenomics.bham.ac.uk/clinicogenomics/
 +
 +
http://pathogenomics.bham.ac.uk/blog/author/nick/
 +
 +
Titus Brown: http://ivory.idyll.org/blog/category/science.html
 +
 +
Lex Nedebragt:
 +
 +
http://contig.wordpress.com/
 +
 +
https://twitter.com/lexnederbragt
 +
 +
Manual Corpas:
 +
 +
Barry L Wanner: https://www.bio.purdue.edu/molecular_biosciences/directory.php?refID=30
 +
*Made many E. coli strains.
 +
 +
Andrew Hessel: http://andrewhessel.com/
 +
 +
===Societies and associations===
 +
 +
Society for applied microbiology: http://www.sfam.org.uk/
 +
 +
American Association for Clinical Chemistry : http://www.aacc.org/Pages/default.aspx
 +
 +
Royal Society of Chemistry: http://www.rsc.org/
 +
 +
Society for general microbiology: http://www.sgm.ac.uk/
 +
 +
American society for microbiology: http://www.asm.org/
 +
 +
Norsk Kjemisk selskap: http://www.kjemi.no/
 +
 +
International Society for Systems Biology: http://www.issb.org/
 +
 +
Genetics Society of America: http://www.genetics-gsa.org/
 +
 +
British Society for Gene and Cell Therapy: https://www.facebook.com/BSGCT
 +
 +
American Society of Human Genetics (ASHG):
 +
 +
Society for Molecular Biology and Evolution (SMBE): http://www.smbe.org/
===Publications===
===Publications===
Line 688: Line 425:
|-
|-
|Bioinformatics||Oxford Journals|| ||http://bioinformatics.oxfordjournals.org/
|Bioinformatics||Oxford Journals|| ||http://bioinformatics.oxfordjournals.org/
 +
|-
 +
|Biology Open||Company of Biologists||Yes||http://bio.biologists.org/
|-
|-
|BMC Medical Genomics||BMC||Yes||http://www.biomedcentral.com/bmcmedgenomics/
|BMC Medical Genomics||BMC||Yes||http://www.biomedcentral.com/bmcmedgenomics/
Line 700: Line 439:
|-
|-
|BMC Microbiology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcmicrobiol
|BMC Microbiology||BioMedCentral||Yes||http://www.biomedcentral.com/bmcmicrobiol
 +
|-
 +
|Cell||Cell Press|| ||http://www.cell.com/
 +
|-
 +
|Cell Reports||Cell Press ||Yes||http://cellreports.cell.com/
|-
|-
|The EMBO Journal||Nature Publishing Group ||No||http://www.nature.com/emboj/index.html
|The EMBO Journal||Nature Publishing Group ||No||http://www.nature.com/emboj/index.html
 +
|-
 +
|Frontiers in Synthetic Biology||Nature Publishing Group|| ||http://www.frontiersin.org/Synthetic_Biology/about
 +
|-
 +
|Genetics||Genetics Society of America|| ||http://www.genetics.org/
 +
|-
 +
|G3: Genes, Genomes, Genetics Mission ||Genetics Society of America|| ||http://www.g3journal.org/
|-
|-
|Genome Research||Cold Spring Harbor Press||Partial (6 month embargo)|| http://genome.cshlp.org/
|Genome Research||Cold Spring Harbor Press||Partial (6 month embargo)|| http://genome.cshlp.org/
 +
|-
 +
|Genome Biology||BMC||Yes||http://genomebiology.com/
|-
|-
|Genome Medicine||BioMedCentral||Yes||http://genomemedicine.com/
|Genome Medicine||BioMedCentral||Yes||http://genomemedicine.com/
 +
|-
 +
|Journal of Experimental Biology||Company of Biologists||http://jeb.biologists.org/
|-
|-
|Journal of molecular biology||Elsevier ||Partial||http://www.journals.elsevier.com/journal-of-molecular-biology/
|Journal of molecular biology||Elsevier ||Partial||http://www.journals.elsevier.com/journal-of-molecular-biology/
Line 711: Line 464:
|Journal of biological chemistry||American Society for Biochemistry and Molecular Biology.  ||No||http://www.jbc.org/
|Journal of biological chemistry||American Society for Biochemistry and Molecular Biology.  ||No||http://www.jbc.org/
|-
|-
-
||Journal of bacteriology||American Society for Microbiology ||No||http://jb.asm.org/
+
|Journal of bacteriology||American Society for Microbiology ||No||http://jb.asm.org/
 +
|-
 +
|Journal of Bioscience and Engineering||  || ||http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
 +
|-
 +
|Journal of clinical microbiology||American Society for Microbiology||No||http://jcm.asm.org/
 +
|-
 +
|mBio||ASM||Yes||http://mbio.asm.org/
 +
|-
 +
|Methods||Elsevier||No||http://www.journals.elsevier.com/methods
 +
|-
 +
|Microbiology||SGM/HighWire Press||No||http://mic.sgmjournals.org/
 +
|-
 +
|Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology Reviews||ASM|| ||mmbr.asm.org
|-
|-
|Metabolic Engineering||Elsevier||Partial||http://www.journals.elsevier.com/metabolic-engineering/
|Metabolic Engineering||Elsevier||Partial||http://www.journals.elsevier.com/metabolic-engineering/
Line 718: Line 483:
|-
|-
|PLOS Computational Biology||Public Library of Science||Yes||http://www.ploscompbiol.org/
|PLOS Computational Biology||Public Library of Science||Yes||http://www.ploscompbiol.org/
 +
|-
 +
|PLOS Pathogens||PLOS||Yes||http://www.plospathogens.org/
|-
|-
|Proceedings of the National Academy of Sciences||National Academy of Sciences||No||http://www.pnas.org/
|Proceedings of the National Academy of Sciences||National Academy of Sciences||No||http://www.pnas.org/
Line 734: Line 501:
|-
|-
|Nature Biotechnology||Nature Publishing Group||No||http://www.nature.com/nbt/index.html
|Nature Biotechnology||Nature Publishing Group||No||http://www.nature.com/nbt/index.html
 +
|-
 +
|Nature Genetics||Nature Publishing group||No||http://www.nature.com/ng/index.html
 +
|-
 +
|Plasmid||Elsevier||No||http://www.journals.elsevier.com/plasmid/
|-
|-
|Journal of Computational Biology||Liebert Publishing||No||http://www.liebertpub.com/CMB
|Journal of Computational Biology||Liebert Publishing||No||http://www.liebertpub.com/CMB
|-
|-
|Trends in Biochemical Sciences||Elsevier|| ||http://www.sciencedirect.com/science/journal/09680004
|Trends in Biochemical Sciences||Elsevier|| ||http://www.sciencedirect.com/science/journal/09680004
 +
|-
 +
|Trends in Microbiology||Elsevier/Cell Press|| ||http://www.sciencedirect.com/science/journal/0966842X
|-
|-
|Molecular Genetics & Genomic Medicine||Wiley||Yes||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
|Molecular Genetics & Genomic Medicine||Wiley||Yes||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
 +
|-
 +
|Molecular genetics and genomics||Springer Verlag|| ||http://link.springer.com/journal/438
 +
|-
 +
|Biochemistry and Molecular Biology Education||Wiley||No||http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
 +
|-
 +
|Current opinion in chemical biology||Elsevier|| ||http://www.sciencedirect.com/science/journal/13675931
 +
|-
 +
|New England Journal of Medicine||NEJM Group|| ||http://www.nejm.org/
 +
|-
 +
|Systems and Synthetic Biology||Springer|| ||http://link.springer.com/journal/11693
 +
|-
 +
|Scientific Reports||Nature Publishing Group||Yes||http://www.nature.com/srep/index.html
|}
|}
Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/
Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/
 +
 +
Computational and Structural Biotechnology Journal
Line 847: Line 634:
===Other informational resources===
===Other informational resources===
 +
 +
National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html
 +
http://seqanswers.com
http://seqanswers.com
Line 1,079: Line 869:
===Protocols===
===Protocols===
 +
 +
http://www.protocolpedia.com/
OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols
OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols
Line 1,113: Line 905:
====Misc. ====
====Misc. ====
 +
 +
http://www.nature.com/scitable
 +
 +
https://www.assaydepot.com/
 +
 +
https://www.scienceexchange.com/
 +
 +
http://matt.might.net
 +
 +
http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html
 +
 +
http://www.phdontrack.net/
Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm
Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm
Line 1,124: Line 928:
http://www.zappylab.com/apps
http://www.zappylab.com/apps
-
Nuclei Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
+
Nucleic Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm
String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn
String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn
Line 1,153: Line 957:
https://genomeinterpretation.org
https://genomeinterpretation.org
-
===Science News ===
+
===Science News & Discussion ===
===Magazines/Blogs/Newssites===
===Magazines/Blogs/Newssites===
 +
 +
http://www.labcritics.com/
 +
 +
http://scienceblok.com/
 +
 +
http://sciblogs.co.nz/
 +
 +
http://www.scicentral.com/index.html
 +
 +
http://blogs.discovermagazine.com/seriouslyscience/
 +
 +
http://epigenie.com/
 +
 +
http://www.livescience.com/
 +
 +
http://scienceblogs.com/
 +
 +
http://scientopia.org/blogs/
 +
The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#
Line 1,163: Line 986:
GEN Magazine: http://www.genengnews.com/
GEN Magazine: http://www.genengnews.com/
-
 
-
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
 
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467
Line 1,177: Line 998:
'''Blogs:'''
'''Blogs:'''
 +
 +
http://ironchefsynbio.wordpress.com/
http://retractionwatch.wordpress.com/
http://retractionwatch.wordpress.com/
Line 1,202: Line 1,025:
http://titojankowski.com/
http://titojankowski.com/
-
Social media:
+
See also http://www.microbe.net/microbiology-blogs/
 +
 
 +
'''Aggregators:'''
 +
 
 +
http://paper.li/SAGRudd/1323661247
 +
 
 +
http://paper.li/leclercfl/bioscience
 +
 
 +
The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246
 +
Norwegian:
 +
 
 +
http://thaliana.blogg.no/1290598240_molekylrbiologi.html
 +
 
 +
Social & personalized media:
http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat
 +
 +
http://trap.it/
 +
 +
 +
'''Discussion sites:'''
 +
 +
http://pubpeer.com/
===In the news/Commentaries===
===In the news/Commentaries===
Line 1,219: Line 1,062:
Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html
Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html
 +
 +
 +
Badomics: http://www.gigasciencejournal.com/content/1/1/6
 +
 +
http://keithbradnam.com/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html
===Jobs===
===Jobs===
Line 1,235: Line 1,083:
http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152
http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152
 +
 +
http://yes.jucan.no/
 +
 +
https://uio.easycruit.com/
 +
 +
 +
Tips:
 +
 +
Search professional/business search sites for companies in fields of interest.
 +
Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.
===Games===
===Games===
 +
 +
BioHack: http://marketplace.xbox.com/en-US/Product/BioHack/66acd000-77fe-1000-9115-d802585505ee
http://eterna.cmu.edu/web/
http://eterna.cmu.edu/web/
Line 1,249: Line 1,109:
http://www.citizensort.org/
http://www.citizensort.org/
 +
 +
http://sourceforge.net/projects/brainworkshop/?source=directory
===Just for Fun===
===Just for Fun===
 +
 +
Origin of the Species in Dub: http://pathogenomics.bham.ac.uk/Dub/origin.html
 +
 +
NCBI ROFL: http://blogs.discovermagazine.com/discoblog/category/ncbi-rofl/
The PCR song: http://www.youtube.com/watch?v=x5yPkxCLads
The PCR song: http://www.youtube.com/watch?v=x5yPkxCLads
Line 1,267: Line 1,133:
Funny bioinformatic tool names: http://www.biostars.org/p/67874/
Funny bioinformatic tool names: http://www.biostars.org/p/67874/
 +
 +
http://abstrusegoose.com
http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/
http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/
 +
 +
Enclothed cognition: http://www.sciencedirect.com/science/article/pii/S0022103112000200
 +
 +
robotniknin: http://www.ncbi.nlm.nih.gov/pubmed/19151731 .
 +
 +
 +
Arxiv vs Snarxiv: http://snarxiv.org/vs-arxiv/
=YouTube=
=YouTube=
 +
 +
https://groups.google.com/forum/?fromgroups=#!topic/diybio/yXfghy7a7wc
 +
 +
 +
http://www.youtube.com/watch?v=mOgTVx9ge5M&feature=player_embedded
 +
 +
 +
http://www.youtube.com/user/basementbiotech
 +
 +
http://www.youtube.com/watch?v=odxvp-3nSw4
 +
 +
Success in Science in 16 minutes: http://www.youtube.com/watch?v=r0vBS0oC8aM
 +
 +
=Favorites=
 +
 +
Favorite things of all kinds:
 +
 +
Bioinformatics blogs:
 +
 +
http://www.homolog.us/blogs/
 +
 +
=To read=
 +
 +
Composability of regulatory sequences controlling transcription and translation in E. coli.

Current revision

Contents

Contact Info

Jarle Pahr
Jarle Pahr
  • Jarle Pahr

jarlemag@alumni.ntnu.no

Education

2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology


Notes

See Notes

Projects

ppGpp MSc. project

Organisms

See Organisms

Interesting articles

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Environmentally controlled invasion of cancer cells by engineered bacteria

Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Genetic programs constructed from layered logic gates in single cells

Research centres/labs

Wyss institute: http://wyss.harvard.edu/

Laboratory for Molecular Infection Medicine Sweden - Umeå: http://www.mims.umu.se/

Cold Spring Harbor Laboratory: http://www.cshl.edu/

Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/

Insititute for Systems Biology: https://www.systemsbiology.org

Virginia Bioinformatics Institute: https://www.vbi.vt.edu/

European Bioinformatics Institute: http://www.ebi.ac.uk/

ATCC: http://www.lgcstandards-atcc.org/

European Molecular Biology Laboratory (EMBL): http://www.embl.de/

http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html


http://unitedscientists.org/labs/norway/NTNU/PhotoSynLab/

http://korflab.ucdavis.edu/

Research programs/projects

Statseq: http://www2.ab.wur.nl/statseq/

Online learning

See Online learning

Language

Synthetic Biology

See Synthetic Biology

Biological part collections

http://partsregistry.org

https://biobricks.org/bpa/find-a-part/

https://registry.synberc.org/

https://public-registry.jbei.org/ (http://www.ncbi.nlm.nih.gov/pubmed/22718978)

DIY Bio/Citizen science

See DIY Bio

http://citizensciencequarterly.com/

Art and Strategy

http://biocouture.co.uk/about/

Xenotext: http://www.law.ed.ac.uk/ahrc/script-ed/vol5-2/editorial.asp

http://en.wikipedia.org/wiki/Christian_B%C3%B6k#The_Xenotext_experiment

http://www.instructables.com/id/Twitter-Mood-Light-The-Worlds-Mood-in-a-Box/

http://blog.arduino.cc/2013/05/19/the-mood-lamp-recognizes-your-facial-expressions-and-turns-them-into-light/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer7d04e

http://thefinchandpea.com/2010/06/20/what-the-end-of-the-world-says-about-science/

http://thefinchandpea.com/2013/08/04/sunday-poem-lord-byrons-post-apocalyptic-vision/

Personal genomics

https://www.23andme.com/

http://www.23andyou.com

http://www.genomesunzipped.org/

uBiome - sequencing your microbiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome

http://www.personalgenomes.org/

Companies

Evolutionary Solutions: http://www.evosol.co/

http://www.allelebiotech.com/allele3/index.php

Era7: http://era7bioinformatics.com/en/index.cfm

DNA electronics: http://dnae.co.uk/

Genome Compiler: http://www.genomecompiler.com/

http://www.strandls.com

http://www.novozymes.com/en/Pages/default.aspx

http://www.genabler.com

http://www.syntheticgenomics.com/

BGI: http://www.genomics.cn/en/index

Gen9: http://gen9bio.com/

DNA 2.0: https://www.dna20.com

Integrated DNA Technologies (IDT): http://eu.idtdna.com/site

GenScript: http://www.genscript.com/

Desktop Genetics: http://www.deskgen.com

Ginkgo Bioworks: http://ginkgobioworks.com/

Biofab: http://www.biofab.org/

http://www.knome.com/

http://www.nucleics.com/

https://www.transcriptic.com/

Cambrian Genomics: https://angel.co/cambrian-genomics http://cambriangenomics.com/

http://www.genologics.com

Suppliers

http://store.p212121.com/

http://www.biosciencetools.com/

http://www.laboratory-journal.com/

www.labx.com

http://www.oxfordgenetics.co.uk/

BioBasic: http://store.biobasic.com/

Promega: http://no.promega.com/

Qiagen: http://www.qiagen.com/

DongSheng Biotech: http://dongshengbio.com/en/index.asp

Macrogen Inc.: http://www.macrogen.com/eng/index/

Carolina Biological: http://www.carolina.com/

Epoch Life Sciences: http://www.epochlifescience.com/Default.aspx

http://www.hometrainingtools.com/

http://www.labsupplymall.com/

United Nuclear: http://www.unitednuclear.com/

New England Biolabs: www.neb.com

Elemental Scientific: http://www.elementalscientific.net/store/Scripts/default.asp

Jena BioScience: http://www.jenabioscience.com/

http://www.synthesisgene.com/

Thermo scientific: http://www.thermoscientific.com/ecomm/servlet/home?storeId=11152

http://www.millipore.com/index.do

See also http://www.made-in-china.com/

Open Biotechnology: http://www.openbiotech.com/

http://www.metabion.com/home/index.php

http://bostonbioproducts.com/

http://www.sbsbio.com/english/dnahc.html

http://www.interfarm.no/produkter/

http://www.iorodeo.com/

Used equipment vendors:

http://www.labrecyclers.com/index.html

Useful links


Conferences and meetings

See Conferences

Scientific challenges and competitions

CAGI - Critical Assesment of Genome Information: https://genomeinterpretation.org/

Assemblathon

Variathon: http://bioinf.dimi.uniud.it/variathon

Alignathon

Sequence squeeze: http://www.sequencesqueeze.org/

Resources for researchers

http://www.protocol-online.org/science-forums-2/Dissertation-and-Paper-Writing/

http://www.protocol-online.org/science-forums-2/Career-Advice/

https://www.researchgate.net

http://friendfeed.com/the-life-scientists

http://nigerianbioscientist.com/

Educational resources

http://www.bioinformatics.nl/molbi/SimpleCloningLab/index.htm

ROSALIND Bioinformatics challenges: http://rosalind.info/problems/locations/

Project Euler: http://projecteuler.net/

AddGene molecular biology reference: http://www.addgene.org/mol_bio_reference/

https://www.manylabs.org/

http://www.dnalabbook.co.uk/

Wiki sites

http://www.scholarpedia.org

SNPedia.com

http://www.wikigenes.org

http://ecoliwiki.net

http://www.phylocommons.org/

Discussion and communities

Apps

mPartsregistry: http://mpartsregistry.appspot.com

Persons/Research groups

http://genefish.wikispaces.com/

Mark Pallen: http://www2.warwick.ac.uk/fac/med/research/microinfect/staff/pallengroup/

Chris Anderson lab: https://andersonlab.qb3.berkeley.edu/

Magni Paolo: http://www.labmedinfo.org/people/magni

http://www.rpgroup.caltech.edu/publications/

Heng Li. "Alignment God".

Dworkin lab: https://www.msu.edu/~idworkin/publications.html

Titus Brown:

Erlich lab: http://erlichlab.wi.mit.edu/index.html

Cristopher mason: http://www.masonlab.net/

http://openwetware.org/wiki/User:Vincent

Markus Gershater

http://www.princeton.edu/~ajlgroup/

Heng Li

Michael Cashel: https://science.nichd.nih.gov/confluence/display/pgd/Michael+Cashel+Lab

Jim Collins: http://www.bu.edu/abl/

Jason Kelly: http://openwetware.org/wiki/Jason_Kelly

Tom Ellis: http://openwetware.org/wiki/User:Ellis

George Church: http://arep.med.harvard.edu/gmc/

Jay Keasling: http://keaslinglab.lbl.gov/research_areas/index.html

Chris Voigt

Bernahrd Ø Pallsson: http://gcrg.ucsd.edu/Researchers/Palsson

Tom Knight

Joe Felsenstein: http://www.gs.washington.edu/faculty/felsenstein.htm

  • Professor of Genome Sciences and Biology, University of Washington.

Drew Endy: http://openwetware.org/wiki/User:Endy

Densmore lab: http://people.bu.edu/dougd/research.html

Ron Weiss: http://groups.csail.mit.edu/synbio/people/professor-ron-weiss/

Jean Peccoud

Jonathan Eisen

Martin Fusenegger

Pamela Silver

Rob Carlson

Ethan Perlstein: http://www.perlsteinlab.com/

Anthony Evans

Nick Loman:

http://pathogenomics.bham.ac.uk/clinicogenomics/

http://pathogenomics.bham.ac.uk/blog/author/nick/

Titus Brown: http://ivory.idyll.org/blog/category/science.html

Lex Nedebragt:

http://contig.wordpress.com/

https://twitter.com/lexnederbragt

Manual Corpas:

Barry L Wanner: https://www.bio.purdue.edu/molecular_biosciences/directory.php?refID=30

  • Made many E. coli strains.

Andrew Hessel: http://andrewhessel.com/

Societies and associations

Society for applied microbiology: http://www.sfam.org.uk/

American Association for Clinical Chemistry : http://www.aacc.org/Pages/default.aspx

Royal Society of Chemistry: http://www.rsc.org/

Society for general microbiology: http://www.sgm.ac.uk/

American society for microbiology: http://www.asm.org/

Norsk Kjemisk selskap: http://www.kjemi.no/

International Society for Systems Biology: http://www.issb.org/

Genetics Society of America: http://www.genetics-gsa.org/

British Society for Gene and Cell Therapy: https://www.facebook.com/BSGCT

American Society of Human Genetics (ASHG):

Society for Molecular Biology and Evolution (SMBE): http://www.smbe.org/

Publications

Journal name Publisher Open access status Link
ACS Synthetic Biology American Chemical Society No http://pubs.acs.org/journal/asbcd6
Bioengineered (Previously: Bioengineered bugs) Landes Bioscience Partial http://dev.landesbioscience.com/journals/bioe/
BioinformaticsOxford Journals http://bioinformatics.oxfordjournals.org/
Biology OpenCompany of BiologistsYeshttp://bio.biologists.org/
BMC Medical GenomicsBMCYeshttp://www.biomedcentral.com/bmcmedgenomics/
BMC ProceedingsBMCYeshttp://www.biomedcentral.com/bmcproc
PLOS One Public Library of Science Yes http://www.plosone.org/
Nucleic Acids Research Oxford Journals Yes http://nar.oxfordjournals.org/
BMC Systems BiologyBioMedCentralYeshttp://www.biomedcentral.com/bmcsystbiol/
BMC MicrobiologyBioMedCentralYeshttp://www.biomedcentral.com/bmcmicrobiol
CellCell Press http://www.cell.com/
Cell ReportsCell Press Yeshttp://cellreports.cell.com/
The EMBO JournalNature Publishing Group Nohttp://www.nature.com/emboj/index.html
Frontiers in Synthetic BiologyNature Publishing Group http://www.frontiersin.org/Synthetic_Biology/about
GeneticsGenetics Society of America http://www.genetics.org/
G3: Genes, Genomes, Genetics Mission Genetics Society of America http://www.g3journal.org/
Genome ResearchCold Spring Harbor PressPartial (6 month embargo) http://genome.cshlp.org/
Genome BiologyBMCYeshttp://genomebiology.com/
Genome MedicineBioMedCentralYeshttp://genomemedicine.com/
Journal of Experimental BiologyCompany of Biologistshttp://jeb.biologists.org/
Journal of molecular biologyElsevier Partialhttp://www.journals.elsevier.com/journal-of-molecular-biology/
Journal of biological chemistryAmerican Society for Biochemistry and Molecular Biology. Nohttp://www.jbc.org/
Journal of bacteriologyAmerican Society for Microbiology Nohttp://jb.asm.org/
Journal of Bioscience and Engineering http://www.journals.elsevier.com/journal-of-bioscience-and-bioengineering/
Journal of clinical microbiologyAmerican Society for MicrobiologyNohttp://jcm.asm.org/
mBioASMYeshttp://mbio.asm.org/
MethodsElsevierNohttp://www.journals.elsevier.com/methods
MicrobiologySGM/HighWire PressNohttp://mic.sgmjournals.org/
Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology ReviewsASM mmbr.asm.org
Metabolic EngineeringElsevierPartialhttp://www.journals.elsevier.com/metabolic-engineering/
Molecular Systems BiologyEMBO/Nature Publishing GroupYeshttp://www.nature.com/msb/index.html
PLOS Computational BiologyPublic Library of ScienceYeshttp://www.ploscompbiol.org/
PLOS PathogensPLOSYeshttp://www.plospathogens.org/
Proceedings of the National Academy of SciencesNational Academy of SciencesNohttp://www.pnas.org/
Protein expression and purificationElsevierNohttp://www.sciencedirect.com/science/journal/10465928
Genome AnnouncementsASMYeshttp://genomea.asm.org/
FuturesElsevier?http://www.sciencedirect.com/science/journal/00163287
Microbial Cell FactoriesBioMedCentralYeshttp://www.microbialcellfactories.com/
Engineering StudiesTaylor & Francis ?http://www.tandfonline.com/loi/test20
FEMS Microbiology Reviews http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6976
Nature BiotechnologyNature Publishing GroupNohttp://www.nature.com/nbt/index.html
Nature GeneticsNature Publishing groupNohttp://www.nature.com/ng/index.html
PlasmidElsevierNohttp://www.journals.elsevier.com/plasmid/
Journal of Computational BiologyLiebert PublishingNohttp://www.liebertpub.com/CMB
Trends in Biochemical SciencesElsevier http://www.sciencedirect.com/science/journal/09680004
Trends in MicrobiologyElsevier/Cell Press http://www.sciencedirect.com/science/journal/0966842X
Molecular Genetics & Genomic MedicineWileyYeshttp://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292324-9269
Molecular genetics and genomicsSpringer Verlag http://link.springer.com/journal/438
Biochemistry and Molecular Biology EducationWileyNohttp://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291539-3429
Current opinion in chemical biologyElsevier http://www.sciencedirect.com/science/journal/13675931
New England Journal of MedicineNEJM Group http://www.nejm.org/
Systems and Synthetic BiologySpringer http://link.springer.com/journal/11693
Scientific ReportsNature Publishing GroupYeshttp://www.nature.com/srep/index.html


Cold Spring Harbor Perspectives: http://cshperspectives.cshlp.org/

Computational and Structural Biotechnology Journal


http://www.journalnetwork.org/journals/science-general/citizen-science/citizen-science-innovation.html

Biotechniques: http://www.biotechniques.com/

https://www.openlibhums.org/

Current protocols in molecular biology: http://onlinelibrary.wiley.com/book/10.1002/0471142727

http://www.g3journal.org/

http://push.cwcon.org/

eLife: http://elife.elifesciences.org/

https://peerj.com/

Faculty of 1000: http://f1000.com/


Social Science Research Network: http://www.ssrn.com/


Open access:

http://en.wikipedia.org/wiki/List_of_open-access_journals

http://scholarlyoa.com/

http://www.doaj.org/

http://www.opendoar.org/

http://blogs.scientificamerican.com/guest-blog/2013/04/03/who-killed-the-preprint-and-could-it-make-a-return/

Publication tools:

https://collage.elsevier.com/

Reference management / Social bookmarking:

http://www.mendeley.com/

http://www.citeulike.org/

JabRef reference manager: http://jabref.sourceforge.net/

Publishers

Springer

Elsevier

CRC Press

Horizon Press

Databases/Repositories

PlasmID database: http://plasmid.med.harvard.edu/PLASMID/

Addgene plasmid repository: http://www.addgene.org/

DNASU plasid repository: http://dnasu.asu.edu/DNASU/

The Open Construct Database: http://www.the-odin.com

Bionumbers - The database of useful biological numbers

EcoCyc - E. coli K-12 MG1655 database: http://www.ecocyc.org/

EcoGene: http://www.ecogene.org

JWS Online model database: http://jjj.biochem.sun.ac.za/database/

http://systems-biology.org/resources/model-repositories/

Genome-Scale metabolic network database: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm

Array express: http://www.ebi.ac.uk/arrayexpress/

Rebase restriction enzyme database: http://rebase.neb.com/rebase/rebase.html

1000 genomes project: http://browser.1000genomes.org/index.html

BRENDA Enzymes: http://www.brenda-enzymes.info/

KEGG

GenBank

http://datadryad.org/

http://www.cathdb.info/

Codon usage

http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333

Codon usage analyzer: http://www.bioinformatics.org/sms2/codon_usage.html

Other informational resources

National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html

http://seqanswers.com

NCBI vs EMBL vs DDBJ.: http://lib.bioinfo.pl/courses/view/151

The DDBJ/EMBL/GenBank Feature Table Definition: http://www.insdc.org/files/feature_table.html#1

http://openwetware.org/wiki/DNA - Contains many protocols

Bite Size Bio: http://bitesizebio.com/

BenchFly: http://www.benchfly.com/

http://biologicalworld.com/protocols.htm

http://www.methods.info/

http://www.biotechdaily.com/

http://www.zenbiology.com/

http://www.my-whiteboard.com/

http://lablife.org

http://www.molbiol-tools.ca/

http://www.molecularinfo.com/MTM/MTM.html

http://www.openhelix.com/ - Genomics and bioinformatics resources.

Programming

BioPython: http://biopython.org/wiki/Main_Page

CodEval - programming challenges: http://codeeval.com/

Law and ethics

http://www.genomicslawreport.com/

American journal of Bioethics: http://www.tandfonline.com/toc/uajb20/current

IASB Code of Conduct for best practices in gene synthesis: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/code-of-conduct-for-best-practices-in-gene-synthesis/

IASB - About Biosafety & Security: http://www.ia-sb.eu/go/synthetic-biology/synthetic-biology/biosafety-biosecurity/

Andrew W Torrance on DNA copyright: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2017670


Cloning

SLIC, Gibson, CPEC and SLiCE assembly methods: http://j5.jbei.org/j5manual/pages/22.html

RF cloning: http://www.rf-cloning.org/QandA.php

PCR Primer design: http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm

PCR: http://www.molbiol-tools.ca/PCR.htm

OpenWetWare - designing primers: http://openwetware.org/wiki/Designing_primers

PCR Guide: http://medicine.yale.edu/labs/henegariu/www/tavi/Guide.html

PCR troubleshooting: http://medicine.yale.edu/labs/henegariu/www/tavi/Trblesht.html

DNA Tm estimation methods: http://openwetware.org/wiki/Primer_Tm_estimation_methods

DNA stability: http://openwetware.org/wiki/DNA_stability

E. coli cloning checklist: http://openwetware.org/wiki/Cloning_Checklist

Guide to Gibson assembly: http://www.synbio.org.uk/dna-assembly/guidetogibsonassembly.html

Primer design guidelines: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html

Sequencing

Design of sequencing primers: http://seqcore.brcf.med.umich.edu/doc/dnaseq/primers.html

Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi: http://biology.duke.edu/fungi/mycolab/primers.htm

GenScript DNA Sequencing Primers Design Tool: http://www.genscript.com/cgi-bin/tools/sequencing_primer_design

Software tools

Molecular Biology Freeware for Windows: http://molbiol-tools.ca/molecular_biology_freeware.htm#Graphic%20packages

Molecular Biology & Bioinformatics Resources: http://library.weill.cornell.edu/eresources/molbio.html

Bioinformatics Tools and Resources for Biomedical Scientists and Students - http://www.changbioscience.com/virtualab.html


DNA copy number calculator: http://www.uri.edu/research/gsc/resources/cndna.html

Graphics software:

Systems Biology

http://systems-biology.org/

Cytoscape: www.cytoscape.org

CAIN stochastic simulations for chemical kinetics: http://cain.sourceforge.net/

COBRA Constraints-based modelling toolbox:

CellNetAnalyzer: http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html

CellDesigner: http://celldesigner.org/

OptFlux: http://www.optflux.org/

Systems Biology Markup Language: www.sbml.org

SBML to LaTex report generator: http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/index.html

Systems Biology Toolbox 2 for MATLAB: http://www.sbtoolbox2.org/main.php

http://www.sysbio.de/

Handbook of Systems Biology: http://www.sciencedirect.com/science/book/9780123859440

Reflexive Systems Biology: http://portal.cbu.uib.no/rsb

Bioinformatics & Annotation

Neural Network Promoter Prediction: http://www.fruitfly.org/seq_tools/promoter.html

Artemis genome browser: http://www.sanger.ac.uk/resources/software/artemis/

BASYS Bacterial Annotation software: http://basys.ca/

SoftBerry: http://linux1.softberry.com/berry.phtml

Promethease: http://snpedia.com/index.php/Promethease

GLIMMER microbial gene-finding system: http://www.cbcb.umd.edu/software/glimmer/

Promoter & termination site search tools: http://molbiol-tools.ca/Promoters.htm

Phyre 2 - protein fold recognition: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

FITBAR DNA binding protein binding site predictor: http://archaea.u-psud.fr/fitbar/

Simple Consensus Maker: http://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html

Model SEED - blog: http://blog.theseed.org/model_seed/

Model SEED - Viewer: http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView

http://www.bioinformatics.org/

Plasmid map drawer: http://www.rf-cloning.org/savvy.php

EMBOSS ((European Molecular Biology Open Software Suite): http://bips.u-strasbg.fr/EMBOSS/

BioBrick -> GenBank converter: http://2010.igem.org/Team:Cambridge/Tools/GenBank


HMMER: http://hmmer.janelia.org/

Jcat Codon Adaption Tool: http://www.jcat.de/

Cloning & Construction

The Constructor: http://2011.igem.org/Team:Wageningen_UR/Softwaretool/

NEBcutter: http://tools.neb.com/NEBcutter2/

J5 automated DNA assembly: http://j5.jbei.org/index.php/Main_Page

Genome Compiler: http://www.genomecompiler.com/

Gibthon: http://django.gibthon.org/


Transcription and Translation: http://www.attotron.com/cybertory/analysis/trans.htm

All-IN-ONE SEQ-ANALYZER: http://www-personal.umich.edu/~ino/blast.html


GENtle 2: http://ec2-23-20-169-157.compute-1.amazonaws.com/dev/#

DNA oligomer design tools:

Primer-BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/

QuickChange primer design script: http://sosnick.uchicago.edu/stuff/quickchanger.pl

IDT SciTools - oligo design and analysis: http://eu.idtdna.com/scitools/scitools.aspx

PrimerDigital: http://primerdigital.com/tools/

Primer3: http://primer3.wi.mit.edu/

Primer3 plus: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

InvitroGen OligoPerfect designer: http://tools.invitrogen.com/content.cfm?pageid=9716

PrimerQuest: www.idtdna.com/Scitools/Applications/Primerquest/

JCVI Primer designer: http://primerdesigner.sourceforge.net/

Primer Design Assistant: http://dbb.nhri.org.tw/primer/index.html

PrimerZ: http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

Primo PCR Primer Design: http://www.changbioscience.com/primo/primo.html

Eurofins PCR primer design: https://ecom.mwgdna.com/services/webgist/pcr_primer_design_new.tcl?ot=OLIGO_PCRD&item_id=new

Eurofins Sequencing primer design: https://ecom.mwgdna.com/services/manage-primers/design-primer.tcl

DNA/oligomer property calculators:

http://www.basic.northwestern.edu/biotools/oligocalc.html

In silico PCR tools:

http://exon.ucsc.edu/cgi-bin/hgPcr

http://insilico.ehu.es/PCR/

http://www.bioinformatics.org/sms2/pcr_products.html

http://qsnp.gen.kyushu-u.ac.jp/genome/InSilicoPCR.html

http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold

http://www.molbiol-tools.ca/Repeats_secondary_structure_Tm.htm

Protocols

http://www.protocolpedia.com/

OpenWetWare protocols - main page: http://openwetware.org/wiki/Protocols

Springer Protocols: http://www.springerprotocols.com

Complementary annealing of oligonucleotides: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html

Knight lab - annealing protocol: http://openwetware.org/wiki/Knight:Annealing_and_primer_extension_with_Taq_polymerase

Knight lab -restriction digest protocol: http://openwetware.org/wiki/Knight:Restriction_Digest

Endy: Colony PCR: http://openwetware.org/wiki/Endy:Colony_PCR

Addgene Moleular cloning guide: http://www.addgene.org/plasmid_reference/index/#cloning

Addgene restriction digest protocol: http://www.addgene.org/plasmid_protocols/restriction_digest/

http://www.addgene.org/plasmid_protocols/bacterial_plates/

http://www.methods.info/Methods/RNA_DNA/restr_analysis.html

http://www.methodbook.net/dna/restrdig.html

Current Protocols: http://www.currentprotocols.com

Science Advisory Board - protocols: http://www.scienceboard.net/resources/protocols.asp?criteria=

Protocol online: http://protocol-online.org/

http://site.methodological.co/

http://bio-protocol.org/

Misc.

http://www.nature.com/scitable

https://www.assaydepot.com/

https://www.scienceexchange.com/

http://matt.might.net

http://www.reportergene.com/2011/10/eln-electronic-lab-notebooks.html

http://www.phdontrack.net/

Misc. molecular biology freeware: http://molbiol-tools.ca/molecular_biology_freeware.htm

J Craig Venter Institute - software: http://www.jcvi.org/cms/research/software/

DNA sequence transformation tools: http://molbiol-tools.ca/Convert.htm

The Oligator: http://gcat.davidson.edu/igem10/tutorial.html

http://www.zappylab.com/apps

Nucleic Acid sequence massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm

String functional protein interaction networks: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=y_1_rGDH3F2_&sessionId=JqYi1VB4HXQn

ProtLifePred protein lifetime calculator: http://protein-n-end-rule.leadhoster.com/

See also: http://2012.igem.org/User_talk:Jarlemag and http://2012.igem.org/Team:NTNU_Trondheim/Links

US National Human Genome Research Institute: http://www.genome.gov/

Codon table: http://en.wikipedia.org/wiki/DNA_codon_table

LaTeX lab book: http://openwetware.org/wiki/LabbookInLatex

Los Alamos Technical Reports collection: http://www.sciencemadness.org/lanldocs.html

http://thelabrat.com

The reproducibility project: http://openscienceframework.org/project/EZcUj/wiki/home

NCBI Coffee Break: http://www.ncbi.nlm.nih.gov/books/NBK2345/

http://www.lablit.com/


Addgene - Genome engineering Guide: https://www.addgene.org/Genome_Engineering/?utm_source=Addgene+March+14%2C+2013+Newsletter+Final&utm_campaign=March+2013+Newsletter&utm_medium=email

https://genomeinterpretation.org

Science News & Discussion

Magazines/Blogs/Newssites

http://www.labcritics.com/

http://scienceblok.com/

http://sciblogs.co.nz/

http://www.scicentral.com/index.html

http://blogs.discovermagazine.com/seriouslyscience/

http://epigenie.com/

http://www.livescience.com/

http://scienceblogs.com/

http://scientopia.org/blogs/

The SynBioLogist: http://paper.li/Socrates_Logos/1306934563#

SciTech Daily: http://scitechdaily.com/

The Scientist: http://www.the-scientist.com/

GEN Magazine: http://www.genengnews.com/

Synthetic biology - Biohacking: http://paper.li/Karelman/1353849467

http://www.reportergene.com/

Super awesome Sylvia: http://sylviashow.com/

http://www.technologyreview.com/

http://www.scilogs.com/

Blogs:

http://ironchefsynbio.wordpress.com/

http://retractionwatch.wordpress.com/

http://www.genomesunzipped.org/

http://ing.dk/blogs/folkeforsker

http://phylogenomics.blogspot.no/

http://88proof.com/synthetic_biology/blog/

http://bytesizebio.net

The hardest science - a psychology blog: http://hardsci.wordpress.com/

http://dienekes.blogspot.no/

Michael Eisen - It's Not Junk: http://www.michaeleisen.org/blog/

Open Helix: http://blog.openhelix.eu/

http://ivory.idyll.org/

http://titojankowski.com/

See also http://www.microbe.net/microbiology-blogs/

Aggregators:

http://paper.li/SAGRudd/1323661247

http://paper.li/leclercfl/bioscience

The Daily Plasmid: http://paper.li/DesktopGenetics/1360025246 Norwegian:

http://thaliana.blogg.no/1290598240_molekylrbiologi.html

Social & personalized media:

http://storify.com/GenomeMedicine/gene-patenting-a-genome-medicine-twitter-chat

http://trap.it/


Discussion sites:

http://pubpeer.com/

In the news/Commentaries

George Church - Reading and writing omes: http://www.nature.com/msb/journal/v9/n1/full/msb201275.html

Synthetic Biology comes down to Earth: http://chronicle.com/article/Synthetic-Biology-Comes-Down/137587/

Predictability - the brass ring for synthetic biology: http://newscenter.lbl.gov/science-shorts/2013/03/13/predictability-the-brass-ring-for-synthetic-biology/

Press Release - Bootstrapping Biotechnology: Engineers Cooperate to Realize Precision Grammar for Programming Cells http://www.synberc.org/bootstrapping-biotechnology

HeLa genome sequenced: http://www.embl-hamburg.de/aboutus/communication_outreach/media_relations/2013/130311_Heidelberg/index.html

Tools for the synthetic biology revolution: http://www.research.gov/research-portal/appmanager/base/desktop;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html


Badomics: http://www.gigasciencejournal.com/content/1/1/6

http://keithbradnam.com/blog/2013/6/23/introducing-jabba-just-another-bogus-bioinformatics-acronym.html

Jobs

https://www.odesk.com/

http://www.tu.no/jobb/

http://www.aftenposten.no/jobb/

http://www.ingeniorstillinger.no/

http://no.indeed.com/jobs?q=Ingeni%C3%B8r&gclid=CJL3_IiL47YCFQdd3godpBMArQ

http://www.nature.com/naturejobs/science/jobs

http://www.teknologijobb.no/jobads/Legg%20til%20i%20filter/Bransje/152

http://yes.jucan.no/

https://uio.easycruit.com/


Tips:

Search professional/business search sites for companies in fields of interest. Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.

Games

BioHack: http://marketplace.xbox.com/en-US/Product/BioHack/66acd000-77fe-1000-9115-d802585505ee

http://eterna.cmu.edu/web/

http://adamilab.msu.edu/evolve-and-conquer/

http://fold.it/portal/

http://phylo.cs.mcgill.ca/ (publication: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031362)

http://io9.com/these-cool-games-let-you-do-real-life-science-486173006

http://www.citizensort.org/

http://sourceforge.net/projects/brainworkshop/?source=directory

Just for Fun

Origin of the Species in Dub: http://pathogenomics.bham.ac.uk/Dub/origin.html

NCBI ROFL: http://blogs.discovermagazine.com/discoblog/category/ncbi-rofl/

The PCR song: http://www.youtube.com/watch?v=x5yPkxCLads

Biorad GTCA song: http://www.youtube.com/watch?NR=1&feature=endscreen&v=ID6KY1QBR5s

iGEM style! http://www.youtube.com/watch?v=KHhswxo6xow

English Tea Time Gene: http://partsregistry.org/Part:BBa_J49005

Trust me, I'm an engineer: http://www.youtube.com/watch?v=rp8hvyjZWHs

I'm an Engineering failure: http://www.youtube.com/watch?v=ro3EPPYbn44

DNA text codec: http://www.sgidna.com/translator.php

Funny bioinformatic tool names: http://www.biostars.org/p/67874/

http://abstrusegoose.com

http://www.davelunt.net/evophylo/2012/12/printing-out-genbank-nucleotide-sequences-1984/

Enclothed cognition: http://www.sciencedirect.com/science/article/pii/S0022103112000200

robotniknin: http://www.ncbi.nlm.nih.gov/pubmed/19151731 .


Arxiv vs Snarxiv: http://snarxiv.org/vs-arxiv/

YouTube

https://groups.google.com/forum/?fromgroups=#!topic/diybio/yXfghy7a7wc


http://www.youtube.com/watch?v=mOgTVx9ge5M&feature=player_embedded


http://www.youtube.com/user/basementbiotech

http://www.youtube.com/watch?v=odxvp-3nSw4

Success in Science in 16 minutes: http://www.youtube.com/watch?v=r0vBS0oC8aM

Favorites

Favorite things of all kinds:

Bioinformatics blogs:

http://www.homolog.us/blogs/

To read

Composability of regulatory sequences controlling transcription and translation in E. coli.

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