From 2010.igem.org
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| | =Weekly Lab Notebook= | | =Weekly Lab Notebook= |
| | ===June 13 – June 19=== | | ===June 13 – June 19=== |
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| | + | '''Colin''' - This week I made a TON of progress with the website. I began working with the template function, which has been a huge timesaver, and generally, makes the whole code look a lot "cleaner". The dropdown menu was a pain, but really is a cool feature! |
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| | + | '''Jeremy''' - This week I began writing the actual branching code. One of the heuristics I was planning on using is the weight of the product in raw atoms, so I have to write associated functions to calculate this and other bits of information. |
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| | + | '''Anna''' - Continued on the Django tutorial found on the Django main website. I was able to create a Django project directory structure for a given project name in the current directory. We learned more about biosynthetic lab techniques. One of the techniques was PCR, which is accomplished due to DNA’s polarity. We learned specific techniques as in the environmental conditions required to accomplish the PCR technique. We also learned more about the basic techniques of plasmid designing. The focus was particularly on primers. The primers are oligonucleotides and which primer you choose has a lot of rules behind it. A part of the length of the primer has to be complimentary, a longer one would be most ideal (20 basepairs). The guanine, cytosine content is important in deciding on a primer. The higher the G-C content, the tigher the primer binds. The nucleotide base composition also determines the melting temperature of the primer-DNA. The forward primer is the primer that sits over the first 18-25 basepairs of the sequence and aligns with the 5’ end, while the reverse primer attaches to the 3’ of the positive end and matches the reverse complement of the forward primer. A program exists online, Microbesonline.org that allows you to select an organism, genes and includes different information. The program gives you operons, domains, homologs, etc. The gene information will give you GC content among other information. We must make sure to check if restriction sites are not in the genes, this can be done by utilizing NebCutter. Choosing a promoter is more like trial and error. Also, don’t forget about the ribosome binding sites which are typically about 12 bp upstream of the gene. Also, it is generally good practice to add a second stop codon to ensure the gene is not read further. A program exists online that designs primers for you based on a desired melting temperatures. |
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| | + | '''Bobak''' - Ironing out bugs from entrez format changes |
| | + | Researching COBRA toolbox, matlab-python interface |
| | + | Implementing and iterating on views in BioMORTAR: imptools and strain designer |
| | + | Performance improvements to enzyme -> gene sequence Entrez lookup |
| | + | Implementing organism enzyme -> gene search and 'closest' organism |
| | + | Implementing PNG -> SVG conversion for plasmid display on server |
Latest revision as of 03:59, 28 October 2010
- The notebook is organized into weeks. Click on the Saturday of each week to view that week's notebook entry
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_May_2010&action=edit 1]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_May_2010&action=edit 3]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_May_2010&action=edit 4]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_May_2010&action=edit 5]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_May_2010&action=edit 6]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_May_2010&action=edit 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_May_2010&action=edit 8]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_May_2010&action=edit 9]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_May_2010&action=edit 10]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_May_2010&action=edit 11]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_May_2010&action=edit 12]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_May_2010&action=edit 13]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_May_2010&action=edit 14]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_May_2010&action=edit 15]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_May_2010&action=edit 16]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_May_2010&action=edit 19]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_May_2010&action=edit 20]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_May_2010&action=edit 21]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_May_2010&action=edit 22]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_May_2010&action=edit 23]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_May_2010&action=edit 24]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_May_2010&action=edit 25]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_May_2010&action=edit 26]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_May_2010&action=edit 28]
| [http://2010.igem.org/UIUC-Illinois-Software/29_May_2010 29]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_June_2010&action=edit 1]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_June_2010&action=edit 2]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_June_2010&action=edit 3]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_June_2010&action=edit 4]
| [http://2010.igem.org/UIUC-Illinois-Software/5_June_2010 5]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_June_2010&action=edit 6]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_June_2010&action=edit 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_June_2010&action=edit 8]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_June_2010&action=edit 9]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_June_2010&action=edit 10]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_June_2010&action=edit 11]
| [http://2010.igem.org/UIUC-Illinois-Software/12_June_2010 12]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_June_2010&action=edit 13]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_June_2010&action=edit 15]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_June_2010&action=edit 16]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_June_2010&action=edit 17]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_June_2010&action=edit 18]
| [http://2010.igem.org/UIUC-Illinois-Software/19_June_2010 19]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_June_2010&action=edit 24]
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| [http://2010.igem.org/UIUC-Illinois-Software/26_June_2010 26]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_June_2010&action=edit 29]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_June_2010&action=edit 30]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_July_2010&action=edit 1]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_July_2010&action=edit 2]
| [http://2010.igem.org/UIUC-Illinois-Software/3_July_2010 3]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_July_2010&action=edit 4]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_July_2010&action=edit 5]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_July_2010&action=edit 6]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_July_2010&action=edit 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_July_2010&action=edit 8]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_July_2010&action=edit 9]
| [http://2010.igem.org/UIUC-Illinois-Software/10_July_2010 10]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_July_2010&action=edit 13]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_July_2010&action=edit 21]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_July_2010&action=edit 22]
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| [http://2010.igem.org/UIUC-Illinois-Software/24_July_2010 24]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_July_2010&action=edit 27]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_July_2010&action=edit 28]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_July_2010&action=edit 29]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_July_2010&action=edit 30]
| [http://2010.igem.org/UIUC-Illinois-Software/31_July_2010 31]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_August_2010&action=edit 1]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_August_2010&action=edit 2]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_August_2010&action=edit 3]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_August_2010&action=edit 4]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_August_2010&action=edit 5]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_August_2010&action=edit 6]
| [http://2010.igem.org/UIUC-Illinois-Software/7_August_2010 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_August_2010&action=edit 8]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_August_2010&action=edit 9]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_August_2010&action=edit 10]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_August_2010&action=edit 11]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_August_2010&action=edit 12]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_August_2010&action=edit 13]
| [http://2010.igem.org/UIUC-Illinois-Software/14_August_2010 14]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_August_2010&action=edit 19]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_August_2010&action=edit 24]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_August_2010&action=edit 25]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_August_2010&action=edit 26]
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| [http://2010.igem.org/UIUC-Illinois-Software/28_August_2010 28]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/31_August_2010&action=edit 31]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_September_2010&action=edit 1]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_September_2010&action=edit 2]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_September_2010&action=edit 3]
| [http://2010.igem.org/UIUC-Illinois-Software/4_September_2010 4]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_September_2010&action=edit 5]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_September_2010&action=edit 6]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_September_2010&action=edit 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_September_2010&action=edit 8]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_September_2010&action=edit 9]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_September_2010&action=edit 10]
| [http://2010.igem.org/UIUC-Illinois-Software/11_September_2010 11]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_September_2010&action=edit 12]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_September_2010&action=edit 15]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_September_2010&action=edit 16]
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| [http://2010.igem.org/UIUC-Illinois-Software/18_September_2010 18]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_September_2010&action=edit 24]
| [http://2010.igem.org/UIUC-Illinois-Software/25_September_2010 25]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_September_2010&action=edit 26]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_September_2010&action=edit 28]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_September_2010&action=edit 29]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_September_2010&action=edit 30]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_October_2010&action=edit 1]
| [http://2010.igem.org/UIUC-Illinois-Software/2_October_2010 2]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_October_2010&action=edit 3]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_October_2010&action=edit 4]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_October_2010&action=edit 5]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_October_2010&action=edit 6]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_October_2010&action=edit 7]
| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_October_2010&action=edit 8]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_October_2010&action=edit 14]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_October_2010&action=edit 28]
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Weekly Lab Notebook
June 13 – June 19
Colin - This week I made a TON of progress with the website. I began working with the template function, which has been a huge timesaver, and generally, makes the whole code look a lot "cleaner". The dropdown menu was a pain, but really is a cool feature!
Jeremy - This week I began writing the actual branching code. One of the heuristics I was planning on using is the weight of the product in raw atoms, so I have to write associated functions to calculate this and other bits of information.
Anna - Continued on the Django tutorial found on the Django main website. I was able to create a Django project directory structure for a given project name in the current directory. We learned more about biosynthetic lab techniques. One of the techniques was PCR, which is accomplished due to DNA’s polarity. We learned specific techniques as in the environmental conditions required to accomplish the PCR technique. We also learned more about the basic techniques of plasmid designing. The focus was particularly on primers. The primers are oligonucleotides and which primer you choose has a lot of rules behind it. A part of the length of the primer has to be complimentary, a longer one would be most ideal (20 basepairs). The guanine, cytosine content is important in deciding on a primer. The higher the G-C content, the tigher the primer binds. The nucleotide base composition also determines the melting temperature of the primer-DNA. The forward primer is the primer that sits over the first 18-25 basepairs of the sequence and aligns with the 5’ end, while the reverse primer attaches to the 3’ of the positive end and matches the reverse complement of the forward primer. A program exists online, Microbesonline.org that allows you to select an organism, genes and includes different information. The program gives you operons, domains, homologs, etc. The gene information will give you GC content among other information. We must make sure to check if restriction sites are not in the genes, this can be done by utilizing NebCutter. Choosing a promoter is more like trial and error. Also, don’t forget about the ribosome binding sites which are typically about 12 bp upstream of the gene. Also, it is generally good practice to add a second stop codon to ensure the gene is not read further. A program exists online that designs primers for you based on a desired melting temperatures.
Bobak - Ironing out bugs from entrez format changes
Researching COBRA toolbox, matlab-python interface
Implementing and iterating on views in BioMORTAR: imptools and strain designer
Performance improvements to enzyme -> gene sequence Entrez lookup
Implementing organism enzyme -> gene search and 'closest' organism
Implementing PNG -> SVG conversion for plasmid display on server
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