http://2009.igem.org/wiki/index.php?title=Special:Contributions/Damfahr2&feed=atom&limit=50&target=Damfahr2&year=&month=2009.igem.org - User contributions [en]2024-03-28T20:55:31ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:Illinois-Tools/ModelingTeam:Illinois-Tools/Modeling2009-10-22T03:46:12Z<p>Damfahr2: /* The Algorithm */</p>
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=='''Modeling'''==<br />
<br />
The Illinois - Tools team can model any pathway, whose starting and ending compounds are stored in the Kegg database. The algorithm developed by the team takes information from the Kegg database and finds the most optimum pathway, based on the weights selected by the user. Examples include the pathway with the least number of steps, or the pathway that uses the least amount of ATP. <br />
<br />
The Illinois-Tools team also wishes to use this algorithm to help other IGEM teams in modeling their own desired pathways. For example, the our program can help the Illinois wetlab team in modeling their pathway. The wetlab team's project is about a binary decoder in the organism E. coli, that senses 2 inputs, such as 2 sugars, and produces one of four possible outputs, which are fluorescent proteins, based on the combination of inputs. <br />
<br />
Go to [https://2009.igem.org/Team:Illinois Illinois] <br />
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A possible future expansion of their project would be to model these pathways computationally, and see if it would be experimentally feasible. Furthermore, once the protein output is obtained, they want to check if it can be used to produce useful compounds like biofuels.<br />
<br />
To help this team reach its goals, our program, IMPtools, was able to model a pathway from D-Arabinose to Ethanol in E. coli. The result can be seen below. It has been optimized for E.coli, and can be further optimized when the wetlab team is ready to work on it. The labels on the reaction are the Kegg IDs for compounds. <br />
<br />
[[Image:Illinoistoolsarabinosetoethanolpathway.jpg|center|]]<br />
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<br />
===The Algorithm===<br />
<br />
In modeling for other teams, a few things should be considered. The algorithm requires interactivity. It is can only optimize if you set the parameters to specify what you mean by "optimal". In that light, the user of IMPtools when modeling for a practical design application should consider how important removing excess reactants or creating biproducts could be, as well as the implications of ATP consumption. Sometimes the algorithm can return intermediate compounds that are truly only cofactors of a main reaction (these can generally be avoided by weighting against high order nodes, but also by specifically removing certain nodes). With IMPtools and a small amount of manipulation, a reasonable pathway can be returned using IMP's pathfinding algorithm. Using these results, actual experimentation is necessary to validate the pathway - perhaps, given future feedback the algorithm could account for user's successes and failures and preferentially bias results toward those experimentally validated.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/ProjectTeam:Illinois-Tools/Project2009-10-22T03:35:45Z<p>Damfahr2: /* Specifications for the next version of IMP tools */</p>
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== '''Overall project''' ==<br />
<br />
<br />
Synthetic biology is the creation of new functions using existing biological systems. In order to assist synthetic biologists, the 2009 Illinois tools team is trying to create a web-based open source program that outputs a theoretical pathway to synthesize a desired chemical product given an input and an output compound. The ideal network will have known reactions taken from the Kyoto Encyclopedia of Genes and Genomes (KEGG)database, which consists of well-studied organisms. The capabilities of our program will be exemplified by establishing a network for the synthesis of a biofuel and a pharmaceutical from various input compounds, as well as the elimination of a toxin. <br />
<br />
Our program is modular and has 4 major components. The first aspect is obtaining reactions from the KEGG database via KEGG API and creating our own database. The second is using all the reactions from our database to create a network. The third is writing the script to assign the appropriate weight to each edge and determining the path of least weight. The fourth is using the resulting pathway to obtain additional information such as a stoichiometric matrix, enzymes that catalyze a specific reaction, and the genes associated with those enzymes. The final step would be to take a feasible pathway and proceed to the lab to test it.<br />
<br />
Click [http://abe-bhaleraolab.age.uiuc.edu/igem/ here] to go to '''IMPtools'''<br />
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== '''Project Details''' ==<br />
<br />
<br />
<br />
<br />
<br />
==Database==<br />
<br />
As mentioned above we used information from the KEGG database to make our metabolic pathway tool. In order to organize the information and be able to retrieve it as desired, we created our own My SQL database with the necessary components for our network. The Kyoto Encyclopedia for Genes and Genomes has his own application programming interface (API) that can be used to allow other software, such as our own, to interact with it.<br />
<br />
Initially we thought that we would create our network using the API functions each time a request was submitted so that we would have the most up-to-date information. Upon testing that out we determined that it would take way too long for each query. This is due to the time it takes to access the database through the API as well as the limited function calls that are available via the API. To fix this problem, we created out own database that has all the information we need it. By doing this, we decreased runtime exponentially. We explored several options and began with sqlite3. This was sufficient for our purposes but in order to ensure robustness for future versions, we switched over to MySQL just before launching our program. <br />
<br />
Using the Django web framework, creating a database was fairly straight forward but precise organization of the database was crucial to keeping runtime and update time to a minimum. After trying several different methods, we settled on creating a database centered on the reaction. Essentially all components can be reached through the reaction model. The picture below depicts the major parts of our database and how they are linked. <br />
<br />
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[[Image:Databasemodels.jpg|500px|center|This picture shows how elements of the database are linked together.]]<br />
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Although we decreased the time it takes for the program to run by creating our own database, there are disadvantages to this method. The biggest disadvantage is that our information will not be as up-to-date as KEGG. KEGG updates parts of their database monthly, other parts weekly, and still others monthly. We decided that in order to keep our program useful we will update our database to ensure that it matches KEGG every two weeks.<br />
<br />
<br />
==Network==<br />
<br />
Using all the information in our database we have created a large network. Our directed multigraph contains all the compounds and their connections. Compound, compound name, and stoichiometry information is stored at each node. The remaining information is stored on the edge. This includes, reaction, reaction name, reversibility, and weight. From reaction we can also access organism, enzyme, and gene information. A visualization of our graph can be seen below. <br />
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[[Image:Networkpic1.jpg|1000 px|center|This is a visualization of our network]]<br />
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[[Image:enlargedv1.jpg|500 px|left]]<br />
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[[Image:enlargedv2.jpg|500 px| right]]<br />
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As you can see in the --- figure, there are some nodes that are very highly connected and others that are barely connected. There ones that are most highly connected are water, ATP, and H+. These are the nodes that we would refrain from using when calculating a pathway. The next pictures are enlarged versions of the pathway showing the information stored in each part.<br />
<br />
==Weighting Scheme==<br />
<br />
By default, our algorithm will find the shortest path from the input compound to the output compound. We realize that this path is not always the path that the user is looking for. In order to allow the scientist further flexibility, we have created the option to weight 6 different constraints that we thought would be useful. Listed below is a description of each constraint.<br />
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'''Fewest Total Reactants/Products'''<br />
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Adding weight to this constraint minimizes the number of reactants and products. This allows minimal disturbance of the natural flux of the organism. <br />
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'''Least ATP Consumption'''<br />
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This weight minimizes the number of reactions that have ATP as a reactant. This allows for a more natural flow of events through the pathway. A pathway that consumes large amounts of ATP would be impractical because organisms can only produce a limited amount of ATP.<br />
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'''Known Enzyme Data'''<br />
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Using this weight limits the number of reactions which do not have enzyme data listed in the KEGG database. Synthetic biology requires that the enzyme and gene data for the reaction is known. If we do not know that information, then we can’t synthetically create a pathway.<br />
<br />
<br />
'''Fewest Changes to Host'''<br />
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When creating a new metabolic pathway, it is important to consider the host in which the organism exists. This weight allows for the fewest changes to the host organism. For example, if the host organism is e.coli, and the fewest changes to host organism constraints is heavily weighted, the program will choose as many pathways that already exist in e.coli as possible in order to get from input to output compound. <br />
<br />
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'''Node Order'''<br />
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This constraint limits the number of nodes that are highly connected. Ideally, we don’t want compounds such as water and ATP, which are in many reactions, appearing in our pathway as primary compounds from the input to the output. By weighting this heavily, a scientist will be able to narrow down the final pathway faster.<br />
<br />
<br />
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When using the program, the user can define up to six different inputs. A dot product of these six inputs against six parameters defined by the program will be used to check each edge of the matrix while assigning the weights. The six parameters defined by the program include: <br />
<br />
<br />
1) number of reactants <br />
<br />
2) number of products <br />
<br />
3) net positive ATP consumption <br />
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4) a 1 if there is no enzyme used, a 0 if there are enzymes used <br />
<br />
5) a 1 if its not in organism, a 0 if within organism<br />
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6) 1 for node order.<br />
<br />
<br />
== Algorithm ==<br />
<br />
The algorithm we used is the bidirectional dikstra. We took this algorithm from graph theory to handle our large data set. The weights are assigned based on the user-defined parameters. This determines the "length" of the edge. Essentially, this algorithm branches out from both the starting and ending compound taking the smallest step possible after calculating the weight of all possible next steps. When the two paths connect you have found the ideal pathway. Although there can be multiple minimal pathways of equal weight, this algorithm guarantees a minimal total weighted pathway between the compounds. <br />
<br />
[[Image:dikstrapic1.jpg]]<br />
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== Results ==<br />
Depending on whether the user specified 1 or 3 pathways, IMPtools will generate and display the top pathway(s). The way it displays the compounds and reactions is through the use of the KEGG ID names that were assigned to them. One could even look these up on the KEGG database for more information using these codes if they wanted to. Now suppose you see a compound that you do not want to be involved in the pathway. Simply click on the "x" button below the compound to tell IMPtools to ignore that compound, and to re-calculate a new pathway. One can also alter the weights that were assigned to the original query and then re-generate a new pathway by clicking update.<br />
<br />
Once you find a path that you like, you are taken to another page in which you will be given the available enzyme and gene data. With this gene data, ideally you could transfect these genes into a host organism that you would grow colonies of, and your new colonies would essentially be able to convert compound A to compound Z. Once you have finished looking at the genes and enzyme data, there will also be a stoichiometric matrix that you could look at. This stoichiometric matrix gives info on what are the costs and products for this pathway.<br />
<br />
To finish up, one can download two different files to keep record and organize their results generated by IMPtools. The first file is a CSV file that one can open up in Microsoft Excel. This document will include compound, reaction, enzyme, and gene data as well as the stoichiometric matrix. Although, this feature is not exactly perfect yet and is still in development. The second file is a text document cantaining XGMML code which can be imported into Cytoscape, a network graphing program. Using Cytoscape, one can view a diagram of the artificial pathway that they created using IMPtools (example below). <br />
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[[Image:Illinoistoolscytoscapeexample.jpg|center|]]<br />
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Compounds are represented by circles, and reactions are represented by squares. The pink circles are the main compounds that are involved in the artificial pathway. The beige circles are the side-products and side-reactants involved in the pathway that are needed for each reaction in addition to the main compounds. The black arrows represent the main pathway, whereas the blue and red arrow represent the production and consumption of side products and reactants respectively. <br />
<br />
Lastly, out program will be able to take the gene data that you generated with IMPtools and export it as Biobrick(s) (adding necessary primers, etc). These one would then submit to the registry. This feature is also under development, and it not perfect. <br />
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== ''' Future Plans''' ==<br />
<br />
== Specifications for the next version of IMP tools ==<br />
<br />
The Illinois software tools team has explored into several new ideas that could potentially become projects for next summer’s team and other future teams. These ideas have focused on adding several new features that improve the present program and expand on what the current project accomplishes. There are several options that the team is currently considering. The user input and feedback that we receive will be taken into much consideration, and based on that, we will decide which changes should be implemented first. In order of importance, the main focus of expansion will be on incorporating the biobrick database, improving graphical representation of pathways, adding more constraints and improving the weighting system, and adding additional helpful features like displaying pricing information on compounds and biobricks, as well as navigational and aesthetic features such as searching compounds directly by name.<br />
<br />
One of the main areas of focus for the future teams will be the inclusion of biobricks and how to make use of the biobrick registry in a better way. This year’s team was able to convert the nucleotide sequence for the genes responsible for a particular pathway into standardized biobricks by cleaving restriction sites, and assigning appropriate prefixes and suffixes. Next year’s team could focus on creating better biobricks that could actually be tested out in an experimental lab. They could research into dividing the biobricks into genes that code for single proteins and enzymes, and ones that code for a series of enzymes that are used in the same pathway. Then, these biobricks can be put together on a single plasmid that contains the code for an entire pathway. <br />
<br />
[[Image:biobricks.png|center|]]<br />
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Another part of the project that can be improved is the graphical representation of the pathways generated. The pathway maps can be provided in a variety of different formats and programs. Some features that could be added are zoom features that could allow users to zoom into pathways and be able to see several alternate paths to a desired compound. This would involve being able recreate and put entire existing databases into one huge map. These interactive maps could be designed by members who are proficient at using software programs like Adobe Flash and Cytoscape. <br />
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[[Image:graphic2.jpeg|300px|center|]]<br />
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Furthermore, next year’s team can improve the pathway generating algorithm by adding more constraints and developing a more efficient weighting system. Global computational studies can be used to evaluate immense numbers of possible input and output combinations. One new method of weighting can be added by assigning price values. This could be used to determine what the most economically valuable metabolic transformation is. Another improvement is picking the right host organism, which contains the highest fraction of the enzymes needed to conduct a transformation. Enzymes from other organisms can also be added to the initial host organism in order to add the desired functionality (considering from which sources the enzyme engineering challenge in the host is likely to be minimized). <br />
<br />
Moreover, some other helpful features that can be added are assigning price values to all compounds and genes used, and then provide a feature that enables users to calculate the total expenses for ordering the compounds needed for a pathway, and also to order biobricks to carry out the pathway reactions in lab. <br />
<br />
These are some of the additional features that could be added to enhance the project. Other ideas that will also be considered are; adding a tutorial that shows users how to create a biobrick if it does not already exist, and a way to favor reactions and pathways that have been genetically altered over time to create a specific product. Another tool that could be added is a flux balance analysis, to balance all the inputs and the outputs of the reaction. Thus, there are several options that are being looked into, for next summer’s team to work on, in order to enhance the current project.<br />
<br />
==== Sources ====<br />
<br />
Pictures:<br />
<br />
http://www.partsregistry.org/Help:An_Introduction_to_BioBricks<br />
<br />
www.biomedcentral.com/1752-0509/2/31<br />
<br />
== The End ==</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/DemoTeam:Illinois-Tools/Demo2009-10-22T03:30:10Z<p>Damfahr2: </p>
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Go to [http://abe-bhaleraolab.age.uiuc.edu/igem/ IMPtools]</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/ResourcesTeam:Illinois-Tools/Resources2009-10-21T23:45:25Z<p>Damfahr2: /* Books */</p>
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As a team who relied mostly on technology, we have a unique list of resources that we either used or investigated. The resources that we looked at can be divided into three categories: Software, Journal Articles, and Books<br />
='''Software'''=<br />
This category includes all programs, libraries, modules, websites, and anything else involving computer technology.<br />
<br />
====Programming Language====<br />
For our web-based program, we used Python 2.5/2.6 programming language in conjunction with the web framework, Django 1.0.2, and MySQL, a relational database management system (RDBMS).<br />
<br />
====Modules/Libraries====<br />
* Biopython<br />
* Networkx<br />
* SciPy<br />
* SoapPy (for KEGG API access)<br />
* Pythongraph<br />
* Pygraphviz (to work with graphviz)<br />
* Pyexcelerator<br />
* Pyopengl<br />
* Matplotlib<br />
<br />
====Websites====<br />
* Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.kegg.jp; our main database that we obtained info from)<br />
* Network Analysis Tools (NeAT; http://rsat.ulb.ac.be/rsat/index_neat.html)<br />
<br />
====Programs/Other====<br />
* Cytoscape (http://www.cytoscape.org/)<br />
* Eclipse<br />
* Graphviz<br />
* Matlab<br />
* COBRA toolbox (for Matlab)<br />
<br />
='''Journal Articles'''=<br />
Becker, Scott; et al.''Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox''.Department of Bioengineering, University of California San Diego.Nature Protocols Vol.2 No.3. March 2007.<br />
*Briefly describes constraint based modeling and give the principles behind it<br />
*Describes the functions of the COBRA toolbox and it explains the output of the program<br />
<br />
Price, Nathan; et al. ''Genome-Scale Models of Microbial Cells: Evaluating the Consequences of Constraints''.Department of Bioengineering, University of California San Diego. Nature Reviews. Vol.2. November 2004.<br />
*Describes the constraints one must take into account when creating genome scale models<br />
*Explains each constraint in detail<br />
<br />
='''Books'''=<br />
Lutz, Mark. <i>Learning Python; 2nd ed.</i> Sebastopol, CA: O'Reilly, 2004. Print.<br />
<br />
<i>Python cookbook; 2nd ed.</i> Beijing: O'Reilly, 2005. Print.<br />
<br />
Minieka, Edward. <i>Optimization algorithms for networks and graphs.</i> New York: M. Dekker, 1978. Print.</div>Damfahr2http://2009.igem.org/IllinoisTools/12_September_2009IllinoisTools/12 September 20092009-10-21T23:34:22Z<p>Damfahr2: /* 9/6-9/12 */</p>
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==9/6-9/12==<br />
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'''Donny''' <br />
<br />
Spent a lot of time just running the calculations and investigated sources of error as well as working on data collection with Nate. After a previous restructuring of the data models there were some lingering problems in the calculations that got resolved this week.<br />
<br />
<br />
'''Nate'''<br />
<br />
I met up with Kanishka this week to talk about ideas for our website. He also had some design ideas for the website, which I considered and applied accordingly to my current design for the website. I also met with Donny and we were able to conclude that my code for data collecting was insufficient for our purposes. It was good for initially collecting data to work with locally, but in order for our online database, we will need code that can collect data and store it automatically while deleting the old database without making use of dictionaries as I have been doing in the past. additionally, my previous code was poorly written as it was, very amateurish and not very efficient. Therefore, I hope to re-write some of my code in a more efficient manner that will be more useful to our website in the form of upodater scripts.<br />
<br />
'''Kanishka'''<br />
<br />
Helped Riyad look for code that allowed to search for restriction enzymes on biobricks</div>Damfahr2http://2009.igem.org/IllinoisTools/5_September_2009IllinoisTools/5 September 20092009-10-21T23:32:31Z<p>Damfahr2: /* 8/30-9/5 */</p>
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==8/30-9/5==<br />
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'''Donny'''<br />
<br />
Debugged the biobrick code written by Riyad and Kanishka (which works well). I also found a way to load a single network when the server is turned on and allows all users to access it without having to pull multiple copies onto memory. This serves not only to speed up the process but also to avoid errors when the back button on the browser is used. <br />
<br />
<br />
<br />
'''Nate'''<br />
<br />
I finished up some work with the CSS and HTML code for our website. It looks really sweet, I can't wait to see it be put up on the internet!<br />
<br />
'''Kanishka'''<br />
<br />
Helped Riyad look for code that allowed to search for restriction enzymes on biobricks</div>Damfahr2http://2009.igem.org/IllinoisTools/29_August_2009IllinoisTools/29 August 20092009-10-21T23:29:19Z<p>Damfahr2: /* 8/23-8/29 */</p>
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==8/23-8/29==<br />
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'''Donny'''<br />
<br />
I worked on improving the graph library to avoid error messages by simply returning false if it is unable to perform the task (a very necessary step to avoid unpleasant webpages).I also focused a lot on assembling a new network that did many calculations ahead of time for faster access later. Now computing weight is performed by a simple dot product without having to query the database. <br />
<br />
<br />
<br />
'''Nate'''<br />
<br />
I was not able to do much this week as it was the first week of class and I also had obligations to fulfill for my new position as a Chem 105 TA. I hope to be able to make more progress in future weeks as I get used to my new class/work schedule.</div>Damfahr2http://2009.igem.org/IllinoisTools/22_August_2009IllinoisTools/22 August 20092009-10-21T23:24:55Z<p>Damfahr2: /* 8/16-8/22 */</p>
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==8/16-8/22==<br />
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'''Donny'''<br />
<br />
I restructured the website for ease of use and aesthetics. In doing so, I was able to clean up some sloppy code that remained from earlier experimentation. I was able to validate Nate's xgmml export feature and found a way to incorporate it into the site.<br />
<br />
<br />
<br />
'''Nate'''<br />
<br />
Worked with the wiki, changing some things. I worked on some graphics that I was hoping to use for the wiki and the website, but I accidentally forgot to save them... Very sad indeed. I also assisted Donny with various codes that I had given him for data collection and the xgmml exporter. I also tried looking up some info about Django, to see if there was anything useful I could learn for our project.</div>Damfahr2http://2009.igem.org/IllinoisTools/8_August_2009IllinoisTools/8 August 20092009-10-21T23:21:46Z<p>Damfahr2: /* 8/1-8/8 */</p>
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==8/1-8/8==<br />
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'''Donny'''<br />
I helped plan the structure of our data models with Palak with a design in mind for the algorithm to utilize the stoichiometry of the reactions. In addition, we decided to regard additional reactants as well as biproducts in separate weighted fields for even more interactivity. <br />
<br />
<br />
'''Palak'''<br />
<br />
This week I found that the way I had set up the database still wasn't good enough because we could not access the stoichiometric information the way we would like. I rearranged our models again and I'm hoping it works this time!!<br />
<br />
'''Nate'''<br />
<br />
This week, I was able to make some progress on the look and feel of our website that will host our webtool, IMPtools. My knowledge of HTML and CSS is very limited, so therefore I relied on a CSS template from the internet that I modified for our purposes. This exercise has been a nice lesson in CSS and how it works in conjunction with HTML. By the end of the week, I was able to get something that could very well become what our website will look like. There are sill some tweaks I need to make, but otherwise the scaffolding of the website is complete.</div>Damfahr2http://2009.igem.org/IllinoisTools/19_September_2009IllinoisTools/19 September 20092009-10-21T23:17:39Z<p>Damfahr2: /* 9/13-9/19 */</p>
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==9/13-9/19==<br />
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'''Donny'''<br />
<br />
Modified the website to return either three paths or only one in order to increase computation time. I also modified the algorithm so that checking for host organism occurred faster, by checking the database rather than having it stored within the network <br />
<br />
<br />
<br />
'''Nate'''<br />
<br />
I worked on the updater scripts for our website. I was able to get one of the two that I need to get done. The first one is for the collection of enzyme data. I was able to successfully write an updater script that is compatible with our webtool and will be able to replace existing enzyme data with new enzyme data. What is nice is that it is really fast too. The other updater script is for the collection of gene data. This will be done next week.<br />
<br />
'''Kanishka'''<br />
<br />
Helped write proposal and future changes to our project for potential donors and organizations that could support us.</div>Damfahr2http://2009.igem.org/IllinoisTools/26_September_2009IllinoisTools/26 September 20092009-10-21T23:14:49Z<p>Damfahr2: /* 9/20-9/26 */</p>
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== 9/20-9/26 ==<br />
'''Donny'''<br />
<br />
I switched the database over from sqlite to mysql so that it can run smoothly with Dr. Bhalerao's server. In this process, I got a chance to verify and utilize Nate's new updater scripts. In addition, I was able to get a more updated version of the network built that incorporated any changes in Kegg.<br />
<br />
'''Riyad'''<br />
<br />
Wrote a biobrick program that analyzes a sequence for biobrick restriction enzyme sites and then adds the associated prefix and suffix<br />
<br />
<br />
'''Palak'''<br />
<br />
I looked at some final features we could add to our program given the time that we have left. We are all busy with school now, it's been hard trying to find time to finish our project. I determined that creating a stochiometric matrix should be feasible. I also gathered some of our old resources and began documenting them in the resources section of our wiki.<br />
<br />
'''Nate'''<br />
<br />
I finished writing the gene data updater script. It was difficult, but I was able to get it done. Once I finished this, I sent this and the enzyme data updater script to Donny for tweaking and integration into our webtool<br />
<br />
'''Kanishka'''<br />
<br />
Helped write proposal and future changes to our project for potential donors and organizations that could support us.</div>Damfahr2http://2009.igem.org/IllinoisTools/17_October_2009IllinoisTools/17 October 20092009-10-21T23:12:58Z<p>Damfahr2: /* 10/11-10/17 */</p>
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==10/11-10/17==<br />
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'''Donny'''<br />
<br />
Launched the website, built the remote database, revised the HTML, implemented the Node Order weighting scheme.<br />
<br />
'''Palak'''<br />
<br />
Worked on the presentation slides. Worked on adding information about the project to the wiki. Met with our advisors and gave a preliminary presentation in order to get feedback. <br />
<br />
'''Riyad'''<br />
<br />
This week I wrote up the safety project and worked on finishing touches to slides<br />
<br />
'''Kanishka'''<br />
<br />
I worked on my part of the slides for the presentation. I also worked on looking into other IGEM teams that were working on similar projects that involved modeling of pathways. This was done to potentially help another team model their pathways computationally, instead of experimentally.<br />
<br />
'''Nate'''<br />
<br />
This week, as the wiki due date draws near, was mostly dedicated to the maintenance of the wiki. I made some graphics that were missing and fixed some that were not quite right. The wiki looks really good now, considering my lack of knowledge of CSS, html, and wikicode. Sure it doesn't look nearly as nice as the wetlab team, but I am still proud of how it looks. At least I got to learn some things about css, html, and wikicode. Also worked on presentation with group this week.</div>Damfahr2http://2009.igem.org/IllinoisTools/24_October_2009IllinoisTools/24 October 20092009-10-21T23:12:20Z<p>Damfahr2: /* 10/18-10/24 */</p>
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==10/18-10/24==<br />
<br />
This week we all worked on final things that need to be done before we arrive in Boston. This includes finishing up the presentation, finalizing the poster, adding features to our program, and testing and debugging final versions of our program. Also, this week our team presented our project to a bioengineering class in order to give them an idea of the opportunities that are available to them.<br />
<br />
'''Donny'''<br />
<br />
I spent a good amount of time tweaking last minute appearance issues and passing any additional files over to the server to make sure that the website will be fully functional for presentation at Boston.</div>Damfahr2http://2009.igem.org/IllinoisTools/26_September_2009IllinoisTools/26 September 20092009-09-26T21:33:08Z<p>Damfahr2: </p>
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== 7/26-8/1 ==<br />
'''Donny'''<br />
<br />
I switched the database over from sqlite to mysql so that it can run smoothly with Dr. Bhalerao's server. In this process, I got a chance to verify and utilize Nate's new updater scripts.</div>Damfahr2http://2009.igem.org/IllinoisTools/26_September_2009IllinoisTools/26 September 20092009-09-26T21:32:22Z<p>Damfahr2: New page: '''Donny''' I switched the database over from sqlite to mysql so that it can run smoothly with Dr. Bhalerao's server. In this process, I got a chance to verify and utilize Nate's new upda...</p>
<hr />
<div>'''Donny'''<br />
<br />
I switched the database over from sqlite to mysql so that it can run smoothly with Dr. Bhalerao's server. In this process, I got a chance to verify and utilize Nate's new updater scripts.</div>Damfahr2http://2009.igem.org/IllinoisTools/1_August_2009IllinoisTools/1 August 20092009-09-26T21:29:33Z<p>Damfahr2: /* 7/26-8/1 */</p>
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== 7/26-8/1 ==<br />
'''Donny'''<br />
<br />
I attempted to use RPAIR data as another potential weight (with the help of Kanishka's research). One helpful thing was to read about other similar applications to determine their weighting scheme. I rearranged our class models to incorporate stoichiometry with Palak and modified the database accordingly. <br />
<br />
'''Riyad'''<br />
<br />
Wrote a program to identify possible trivial compounds by seeing how many compounds go into and come out of a given compound and then going through the top 100 compounds and deciding which seemed trivial or not.<br />
<br />
'''Palak'''<br />
<br />
This week I spent time getting stoichiometry information about the into our database. We decided to incorporate a stoichiometric matrix as part of our program output. I also rearranged some of our models so in order to incorporate the stoichiometric information properly. <br />
<br />
'''Kanishka'''<br />
<br />
I read articles to find a weighing system and found how to incorporate weights with different point values. I also spent time on developing the webpage.<br />
<br />
'''Nate'''<br />
<br />
In the beginning of the week, I worked on examining certain reactions that required multiple enzymes to facilitate them. One reaction had as many as 66 different types of enzymes needed!! This is a little ambiguous point about KEGG and/or the naming of enzymes. It is hard to discern if the types of enzymes listed for a reaction are either all needed (they are all subunits), or some of them are interchangeable (the organism makes two different enzymes that facilitate the same reaction). After reporting my findings to Donny, I set work on writing code that would ideally export the data obtained with IMPtools in a xgmml file format. Xgmml is a coding language that specifies a graph of nodes and edges. This type of code is recognized by Cytoscape, a program that we had looked at in the beginning of the summer. We have recently decided to use cytoscape for graphically representing the outputs of IMPtools. I was very successful with my program, as it makes a nice, easy to see graph of any reaction pathway. I sent this code to Donny, so that he may work it into our website. This has been a super fun summer!</div>Damfahr2http://2009.igem.org/IllinoisTools/25_July_2009IllinoisTools/25 July 20092009-09-26T21:24:26Z<p>Damfahr2: /* 7/19-7/25 */</p>
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== 7/19-7/25 ==<br />
'''Donny'''<br />
<br />
I worked with Nate on exporting the results of the web page (specifically CSV). I also spent a large amount of time reorganizing the website (for easier navigation and also to more clearly display the results). <br />
<br />
'''Nate'''<br />
<br />
This week, I worked a lot on the design of our wiki. Now that we have finally decided on a name for our web-tool, IMPtools, I was able to create a logo for our website. This logo I have also included on our wiki. In addition to this logo, I have also developed more graphics to personalize each section of our wiki page. I also redesigned our navigation bar, as the old one was a bother. Towards the end of the week, I also worked on the possibility of CSV file export for our web-tool. Ideally, we hope to be able to export a user's results/data in a CSV file format so that they can open it up in Microsoft Excel. I was not so successful with this, but fortunately Donny was able to figure out how to get a csv file to be exported from our web-tool. Now all we need to do is format the file that is to be exported. We still have a lot of work to do for our web-tool, such as the look and feel of the website.<br />
<br />
'''Palak'''<br />
<br />
Over past few days I took the dictionaries that Nate assembled and put them in our database. I also spent some time taking the scripts he wrote to assemble the dictionaries and turning them into scripts that would update the database. I ran into difficulty trying to write some of them such that they only updated the database rather than rewriting the whole thing.</div>Damfahr2http://2009.igem.org/IllinoisTools/18_July_2009IllinoisTools/18 July 20092009-09-26T21:21:43Z<p>Damfahr2: /* 7/12-7/18 */</p>
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==7/12-7/18 ==<br />
'''Donny'''<br />
<br />
I modified the graph library to add room for additional weights. I also added search fields rather than drop down menus for selecting the desired compound.<br />
<br />
'''Nate'''<br />
<br />
This was also a very productive week. I was able to get a slew of programs written that I ended up combining to collect and organize data from the KEGG in ways that are most beneficial to our goals. Using this master program, I have assembled a few dictionaries that we can use for our web-tool. Here are the types of dictionaries I have made using my master program:<br />
<br />
-Organism Enzymes to Genes (specify organism and enzyme, and it returns the gene)<br />
<br />
-Enzymes to Organisms (specify enzyme, and it returns the organisms that the enzyme has genes in)<br />
<br />
-Reactions to Enzymes (specify reaction, and it returns the enzymes that facilitate that reaction)<br />
<br />
-Enzymes to Genes (specify enzyme, and it returns all genes that can encode that enzyme that are listed on KEGG)<br />
<br />
<br />
The great thing about this master program is that it is super fast! Hurray for python! Also, I changed the colors for our wiki, and fixed it up a bit. Now it looks a lot better than before (as everybody liked the colors better this time around...).<br />
<br />
<br />
'''Palak'''<br />
<br />
This week I continued to populate the database with information from KEGG such as reaction reversibility, reactants, products, etc. I worked particularly long on creating a script to update reversibility because I ran into problem being able to check if it had been changed on the KEGG database.</div>Damfahr2http://2009.igem.org/IllinoisTools/18_July_2009IllinoisTools/18 July 20092009-09-26T21:21:31Z<p>Damfahr2: /* 7/12-7/18 */</p>
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==7/12-7/18 ==<br />
'''Donny'''<br />
I modified the graph library to add room for additional weights. I also added search fields rather than drop down menus for selecting the desired compound.<br />
<br />
'''Nate'''<br />
<br />
This was also a very productive week. I was able to get a slew of programs written that I ended up combining to collect and organize data from the KEGG in ways that are most beneficial to our goals. Using this master program, I have assembled a few dictionaries that we can use for our web-tool. Here are the types of dictionaries I have made using my master program:<br />
<br />
-Organism Enzymes to Genes (specify organism and enzyme, and it returns the gene)<br />
<br />
-Enzymes to Organisms (specify enzyme, and it returns the organisms that the enzyme has genes in)<br />
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-Reactions to Enzymes (specify reaction, and it returns the enzymes that facilitate that reaction)<br />
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-Enzymes to Genes (specify enzyme, and it returns all genes that can encode that enzyme that are listed on KEGG)<br />
<br />
<br />
The great thing about this master program is that it is super fast! Hurray for python! Also, I changed the colors for our wiki, and fixed it up a bit. Now it looks a lot better than before (as everybody liked the colors better this time around...).<br />
<br />
<br />
'''Palak'''<br />
<br />
This week I continued to populate the database with information from KEGG such as reaction reversibility, reactants, products, etc. I worked particularly long on creating a script to update reversibility because I ran into problem being able to check if it had been changed on the KEGG database.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week7Team:Illinois-Tools/Notebook/Week72009-08-03T21:29:55Z<p>Damfahr2: </p>
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==7/5- 7/11==<br />
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'''Donny'''<br />
<br />
I created a graph library which I call dongraphlib to handle our specific functions. I took a look of code from NetworkX and pygraph but made modifications and left out everything we have no need for. I included a bidirectional dijkstra algorithm to make the shortest path calculation go extremely fast (less than a second!).<br />
<br />
'''Palak'''<br />
<br />
This week I worked on creating a script that would determine whether or not the reaction is reversible. I also worked on a few administrative tasks. I spoke with the Office of the Vice Chancellor of Research to discuss what kind of support they could provide us. I also took a look at a few grants that we could apply for in order to get funding for next year.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week11Team:Illinois-Tools/Notebook/Week112009-08-03T21:13:07Z<p>Damfahr2: New page: {{Illinois-Tools/Template1}} :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week10 <<previous week] [http:...</p>
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==8/2-8/8 ==<br />
'''Donny'''</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week10Team:Illinois-Tools/Notebook/Week102009-08-03T21:12:24Z<p>Damfahr2: New page: {{Illinois-Tools/Template1}} :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week9 <<previous week] [http:/...</p>
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== 7/26-8/1 ==<br />
'''Donny'''</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week9Team:Illinois-Tools/Notebook/Week92009-08-03T21:11:35Z<p>Damfahr2: New page: {{Illinois-Tools/Template1}} :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week8 <<previous week] [http:/...</p>
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== 7/19-7/25 ==<br />
'''Donny'''</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week8Team:Illinois-Tools/Notebook/Week82009-08-03T21:10:56Z<p>Damfahr2: New page: {{Illinois-Tools/Template1}} :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week7 <<previous week] [http:/...</p>
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==7/12-7/18 ==<br />
'''Donny'''</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week7Team:Illinois-Tools/Notebook/Week72009-08-03T21:10:04Z<p>Damfahr2: New page: {{Illinois-Tools/Template1}} :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week6 <<previous week] [http:/...</p>
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==7/5- 7/11==<br />
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'''Donny'''</div>Damfahr2http://2009.igem.org/Team:Illinois-ToolsTeam:Illinois-Tools2009-07-21T02:16:24Z<p>Damfahr2: </p>
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<li><a href="https://2009.igem.org/Team:Illinois-Tools" class="active">Home</a></li> <br />
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<li><a href="https://2009.igem.org/Team:Illinois-Tools/Project">The Project</a></li> <br />
<li><a href="https://2009.igem.org/Team:Illinois-Tools/Parts">Parts</a></li> <br />
<li><a href="https://2009.igem.org/Team:Illinois-Tools/Modeling">Modeling</a></li> <br />
<li><a href="https://2009.igem.org/Team:Illinois-Tools/ResearchArticles">Research Articles</a></li> <br />
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We are the 2009 University of Illinois Tools Track Team; <br> project description and more to be added!<br />
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{|align="justify"<br />
|This is the first software tools team from Illinois. We are comprised of Biology, Bioengineering, and Chemical Engineering majors. With limited programming and synthetic biology experience we have been learning a lot along the way. <br />
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Our tool will utilize the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. We will most likely create a list of toxic pollutants as our input to the pathway and have value added products such as biofuels as the product. The goal is to create a network of reactions that connect our input to output and then to determine an optimal path. We are going to focus this task on one or two hosts (most likely E. Coli or Yeast). Constraint based reconstruction analysis (COBRA) will be used to determine the production rates of our product. The goal is to hopefully link together reactions in such a way that production and biomass growth are working together (thus it is favorable for the host to be producing). Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures. <br />
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{{CURRENTVERSION}}</div>Damfahr2http://2009.igem.org/User:Damfahr2User:Damfahr22009-07-18T19:29:02Z<p>Damfahr2: </p>
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<h2>Donny Amfahr</h2><br />
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[[Image:Donny.jpg | right | 250px]]<br />
I am a rising junior in Chemical Engineering with a minor in Computer Science. I will be acting as the Science Director of our group and am enjoying my first iGEM experience so far. I'm really excited to see our project progress over the next few months. I am also looking forward to learning more about synthetic biology and new programming languages. <br />
<br />
Outside of the classroom I enjoy playing lacrosse, working on my first iPhone app, and hanging out with Adrienne.<br />
<br />
[[Team:Illinois-Tools/Team|Back to Team Page]]</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week6Team:Illinois-Tools/Notebook/Week62009-07-14T22:14:21Z<p>Damfahr2: </p>
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== 6/28-7/4 ==<br />
'''Donny'''<br />
<br />
At this time, I have a working prototype for the site. It has a user interfaces with forms and/or dropdown menus to select the desired compound. From there the site will return the shortest path (by number of reactions). It displayed the KeggID and common name of each intermediate, as well as the reaction ID's that correspond to the returned pathway. It's final feature to date, is listing the cofactors and additional substrates that were assumed to be present for the pathway to succeed. <br />
<br />
'''Kanishka'''<br />
<br />
Biobricks!! - The goal of our project will be to provide the user with all the biobricks that code for all the enzymes needed for a particular reaction pathway. So first, we will have to figure out the genes that code for all the enzymes that will carry out a particular pathway. First, we will take the nucleotide sequences for these genes and check whether the exact sequence already exists in the existing biobrick database. So we will have to scan through the biobrick registry to compare our sequences with the existing sequences. Since the current biobrick registry only has about 3200 parts, it is highly unlikely that the exact sequence will already be existing. However, if any of the sequences do already exist, the program will tell the user that the biobrick for that particular gene already exists, and for the remaining sequences, the program will construct biobricks for all these genes and display them for the user. Now from what I think, each biobrick will be one gene. (Because one enzyme cant come from two different genes, but one gene can code for several proteins). Each gene can either code for a single enzyme, or multiple enzymes. So if a particular reaction pathway contains 20 enzymes, there may be up to 20 different biobricks. The program will add the appropriate suffix and prefix to the sequences, assign them to a biobrick standard, and then present them in a proper biobrick format. (Now Im not sure if we could combine these biobricks into one biobrick, since all the biobricks code for one reaction). So the user then can order all these biobricks, and then in lab, can insert these plasmids into a bacteria and carry out the particular reaction. If we can, we should actually test this out in lab with the help of the wetlab team.<br />
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'''Riyad'''<br />
Worked with Kanishka on biobricks. He pretty much did an excellent job summing it up so not much to add. Right now we are looking into incorporating sometype of BLAST into our program to compare our output gene sequence with the biobrick registry.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week5Team:Illinois-Tools/Notebook/Week52009-07-14T21:54:50Z<p>Damfahr2: </p>
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== 6/21-6/27 ==<br />
'''Donny'''<br />
<br />
During this week I put a lot of focus into writing code to update our database. Eventually, we will be able to re-use some of this code in an automated process that keeps our network up to date with the Kegg database. <br />
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'''Kanishka'''<br />
I'm chill !!! (ok, everyone needs to give a one word description of themselves) ......... worked on Biobricks!!</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week1Team:Illinois-Tools/Notebook/Week12009-07-02T20:57:26Z<p>Damfahr2: </p>
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== 5/24-5/30 ==<br />
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<br />
The team developed a better idea of how we are to make this software thanks to the advice and guidance from Professor Bhalerao.<br />
<br />
'''Donny'''<br />
<br />
I spent the week brainstorming possible ideas and applications of our project as well as researching some of the considerations we might need to account for. I also looked into what software tools have been made in the past to ensure originality of our design. We made a list of "Donny's Crazy Ideas" for the project. After a lot of brainstorming, we decided to stick with our original idea after all, but the planning process was very beneficial because it gave some direction on how to get started. <br />
<br />
Im not sure what Nate thinks he will get by sucking up to me, but I don't trust him for a second. <br />
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'''Nate'''<br />
<br />
Nate learned some fun basic stuff about Python. Also, he looked into graphical options that we hope to use in the future in conjunction with our program with help from Kanishka. Graphviz was the main application investigated, as well as the modules that would be needed to run it via Python, such as Pydot, Pygraphviz, and Networkx. Not sure what Donny is talking about, given that the software has yet to be written. However, he is very thankful to have Donny "The Ultimate Programmer" Amfahr on the team for his infinite knowledge and wisdom about programming and such.<br />
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'''Palak'''<br />
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I read papers by Dr. Price about constraint based modeling and the factors that need to be taken into account when genome-scale models are created. I also read another paper that described a program called COBRA that is used for constraint based modeling. I began learning how to program in python.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week2Team:Illinois-Tools/Notebook/Week22009-07-02T20:57:12Z<p>Damfahr2: </p>
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== 5/31-6/6 ==<br />
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'''Donny'''<br />
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This week, I learned the basics of the python programming language. I spend most of my time working with the Kegg API to access data via the SOAP protocol. I was able to utilize this new information to create a module that converts the common name to a usable kegg_id and also to convert the kegg_id back to a name. One concern I have is that even these simple functions are somewhat slow. Perhaps we will find ways to speed these processes up in the weeks to come. I looked into the possibility of Google App Engine. The one shortcoming (although it is pretty cool) was that there were some restrictions as to which libraries can be used. I foresee this as a problem and am looking into other options. <br />
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'''Riyad'''<br />
<br />
We got Cobra working so I spent the majority of the week getting used to how Python and Cobra worked.<br />
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'''Palak'''<br />
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I began working with the various functions in COBRA. I spent a lot of time understanding the output of COBRA and determining what aspects are necessary in creating an optimal pathway. I also looked at the inputs required for various COBRA functions and looked into ways that we can pass information from the KEGG database into COBRA. I figured out how to use the KEGG API. Additionally, I spend some time looking at the COBRA source code to see what we could modify to fit the needs of our program.<br />
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'''Nate'''<br />
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Since last week, I had some difficulties with installing python modules, specifically the ones that would allow us to graphically represent our program's outputs. Tried to get a program called Easy_Install to work, which would make installing modules easy, but it was difficult to figure out how to get Easy_Install to install... Fortunately, Donny was able to find an easy way to install the modules via MS-DOS prompt on windows. Now I am able to install any module...almost.<br />
I ended up installing these modules:<br />
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-Networkx<br />
<br />
-Pydot<br />
<br />
-Matplotlib<br />
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As well as these additional programs:<br />
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-Graphviz<br />
<br />
-Cytoscape<br />
<br />
Up to this point we have been using Python 2.6, but unfortunately I was unable to get all of the above modules to install correctly for Python 2.6. I downgraded to Python 2.5, and was able to get all of the modules to install and work properly. I was finally able to generate a graph via Python in conjunction with Graphviz!! I also experimented more with Cytoscape, another graphing program that we could use. However, Cytoscape does not appear to be compatible with Python at the moment. We probably will not be using Cytoscape.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week3Team:Illinois-Tools/Notebook/Week32009-07-02T20:56:52Z<p>Damfahr2: </p>
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== 6/7-6/13 ==<br />
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'''Donny'''<br />
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We have considered using toxic chemicals as inputs to our program to suggest a pathway that would convert harmful pollutants into valuable chemicals. I wrote a script that scans a list of harmful chemicals from the EPA and then forms a dictionary pairing the chemical name to its KEGG_ID. The script doesn't quite work perfectly and not all chemicals are found on Kegg. This will be improved throughout the week. Also, I am looking into the possibility of using django to host our application on the web.<br />
<br />
I was finally able to figure out who that girl is that I saw in the gatehouse and at work. Potential suspects were Lucy from the other team or Jacinda the secretary. After extensive facebook searches, the unlikely candidate of Julie Richards turned out to be the culprit. I look forward to meeting her or something so I feel less strange about all the stalking<br />
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'''Riyad'''<br />
Read articles related to metabolic pathways and biological networks to better understand how fluxes work. Also messed around with the Flux Balance Analysis in the COBRA toolbox.<br />
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'''Kanishka'''<br />
Worked on learning the python language through tutorials and textbooks.<br />
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'''Nate'''<br />
Explored the world that is wiki. I learned some useful things about wikis(such as templates), and investigated ways to create and edit our wiki page. Looked into some programs, such as dreamweaver, but I am not sure if that will really be of any help with the wiki. I also learned some fun stuff about Linux, and learned some linux commands via Cygwin, a linux emulator for windows. Lots of fun indeed! Towards the end of the week, I learned a great deal about Python programming. In particular, I learned about for and while statements, classes, def statements, regular and global variables, lists and strings. This will be very useful in the future. I was also able to write some small programs. These included a number guesser program(user gives input of what to add and subtract to get to the goal) and a prime number generator. These very basic programs are not very useful of course, but they allowed me to better understand the programming language. Can't wait to start writing some useful code. Also, watching Donny stalk people on facebook has been very entertaining.<br />
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'''Palak'''<br />
I determined that one of the necessary elements in determining ideal pathway was flux balance analysis. I spent sometime looking into what the flux of a reaction is as well as how it is calculated. It turns out that the function in COBRA that finds the flux balance analysis uses a linear solver. I experimented with various linear solvers that are compatible with python interpreters. I found the NUMpy and SCIpy were the most useful modules. I also continued to learn how to program in python using several tutorials.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week4Team:Illinois-Tools/Notebook/Week42009-07-02T20:56:27Z<p>Damfahr2: </p>
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== 6/14-6/20 ==<br />
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'''Donny'''<br />
<br />
I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palak found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production. <br />
<br />
In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).<br />
<br />
<br />
<br />
'''Ankit'''<br />
<br />
So after receiving Donny's intimidating email, I finally feel like I should write in the lab notebook. I am still without my laptop, which makes it harder to work on code. But for the last week I have been working on getting COBRA sources codes uploaded to our program. I found a program called OMPC. Apparently, OMPC allows running MATLAB®'s m-files using Python interpreter. OMPC reads m-files and translates them into Python compatible code.<br />
<br />
Note having a laptop, I have been unable to check if this program works. Hopefully my laptop comes in tomorrow, so I can check this out because it will save us a lot of time by note having to convert about 30-40 COBRA source codes written in MATLAB to Phyton. <br />
<br />
Moreover, I am still concerned with our project. It seems as we are just doing what the Maranas group has already done with the OptStrain (OptStrain: a computational framework for redesign of microbial production systems. {Maranas 2004}). It seems like they have already done what we have done but their code is in GAMMS and isn't an open source program. Hopefully when our program is done, we will have some awesome cool features.<br />
<br />
<br />
<br />
P.S. on a unrelated note and knowing that none technicians that are currently repairing my laptop are reading this, I just like to say that I WANT MY LAPTOP NOW!<br />
<br />
'''kanishka'''<br />
<br />
Last week I had the MCATS so I took a little break, but now I'm back. I've been trying to learn python and have been following Dr Bhalerao's book, "Python Cookbook". My goal is to finish the book by the end of the week and learn some cool stuff. I will also refer to another book that I have torrented (shhh!, downloaded), "Programming Python". I have also been messing around with the Kegg API and tried to figure out how it works.<br />
<br />
'''Riyad'''<br />
This week I learned a good deal about making stand alone matlab functions. This would allow us to use the COBRA functions outside of a matlab environment. I also started doing research into the S-matrix and found some matlab functions that might come into future use. I continued to get familiar with python and made a random letter generator that spits out "A" "T" "C" and "G" ,randomly... It was fun to make but not sure how practical it is<br />
<br />
'''Nate''''<br />
<br />
This week has been very exciting in terms of coding and programming. I had fun learning about dictionaries and how to make them and use them in Python. I was also able to manipulate the Kegg database in a number of ways through the KEGG API. Looking through the KEGG API, there are many commands, such as get_reactions_by_enzyme, and get_enzymes_by_compound. However, I realized there is no command to get_reactions_by_organism. Since our program will go from compound A to compound B through the various reactions listed on KEGG, I felt this type of function would be very useful to us. This would be useful in determining a host organism by seeing which organisms each reaction can take place in. Therefore, using the new tools I had learned for Python and the KEGG API I started making programs that compiled lists of information from the KEGG database that I could use to perform this organisms, and hopefully vice versa for get_organisms_by_reaction. Before I started making code, I made a map of going from Organsims, to genes, to enzymes, and finally to reactions. My first task was to compile a list of Organsims and the 3 or 4 letter codes that KEGG has assigned to each organism. These code names are needed when doing certain queries to the KEGG API. In particular, I needed this list of code names for the Organisms to genes step via the command get_genes_by_organisms. I ended up writing my code to retrieve all of the genes by code name for every organism listed on the KEGG database and compiled these lists of genes for every organism into one HUGE list of lists. I ended exporting this extremely large list of lists of genes by organism to a text file via the pickle module for python. This text file is the biggest text file I have ever seen, coming in around 200 MB. LOL.... This program also took a long time to run as well, took about 3 or 4 hours to finish. Since this list is so huge, I decided to just work with Ecoli for now, and move on to S cerevisiae and other organisms later. My next step was to get enzymes by genes. I did this for Ecoli only, and compiled and exported the list to a txt file. This also took quite some time. I started working on getting reactions by enzyme, when I learned something interesting, yet annoying. Enzymes are given a code name in the form of 'ec:1.1.1.3' on the kegg database. This code name is "non-organism" specific. Therefore, getting reactions by enzyme has the potential of retrieving reactions that do not occur in Ecoli, since the enzyme name is a generic name for any enzyme that performs a reaction. Sometimes, enzymes can facilitate more than one reaction. In terms of Ecoli, not all of these reactions that an enzyme can perform can necessarily occur in Ecoli. Therefore, I discovered I must find another way that will be organism specific throughout the whole process of going from organism to reaction. My new flow was now from organism, to gene, to ko number (orthology?? not fully uderstood), to pathway, to reactions that occur in pathway. I got all the way through to reactions for Ecoli, but I realized I had another problem. Yes, I had a list of reactions for Ecoli, but I did not know which gene was associated with what reaction. That I realized is very important to know; what genes are associated with what reactions. This will be very useful for our program. To my dismay, I could not think of a way to get reactions by gene and vice versa through the KEGG API alone. Therefore, I used the KEGG FTP to obtain a list of reactions, that I hope to get enzymes for, and then the genes for all of those enzymes. This I will work with next week. On a side note, I thought of some fun features that we could have as a part of our program. One idea I had was converting genes that qualify from the KEGG database into biobricks by basically adding the DNA needed to fulfill the state of being a 'biobrick'. Another idea I had was to optimize all of the genes that are to be outputted by our program for the host organism that is chosen by user through codon optimization. Each organism has varying levels of charged tRNAs. The idea would be to alter the codons so that the percentage of each codon reflects the percentage of the charged tRNAs. Right now, these ideas are still being considered, they might be fun to do once our program is finished.<br />
<br />
'''Palak'''<br />
This week the changed the direction of our project slightly. We decided that we would add an option that allowed the user to choose a shortest path depending on a chosen factor such as lowest energy usage or least number of cofactors. This allowed us to create graphs of the reactions with weights. We would then find the path of least weight for the given factor. This eliminated the need to find all paths, which we found wasn't feasible. Due to this the need for flux analysis functions was not crucial right away. I put this part of the project on hold and started working on another aspect, creating databases. We found that it would speed up our program if we had our own database of reactions and their properties. I explored different possibilities to create this database. We work with MySQL and SQLite. Ankit and I determined that SQLite was sufficient for our purposes. The two of us, spent the rest of the week learning how to use SQLite3 and integrate it with Django.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week5Team:Illinois-Tools/Notebook/Week52009-07-02T20:56:09Z<p>Damfahr2: </p>
<hr />
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<br />
== 6/21-6/27 ==<br />
'''Donny'''<br />
I'm awesome</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week6Team:Illinois-Tools/Notebook/Week62009-07-02T20:55:53Z<p>Damfahr2: </p>
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== 6/28-7/4 ==<br />
'''Donny'''<br />
I'm awesome</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week6Team:Illinois-Tools/Notebook/Week62009-07-02T20:51:59Z<p>Damfahr2: /* 6/28-7/4 */</p>
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== 6/28-7/4 ==<br />
'''Donny'''<br />
I'm awesome</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week5Team:Illinois-Tools/Notebook/Week52009-07-02T20:51:38Z<p>Damfahr2: /* 6/21-6/27 */</p>
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== 6/21-6/27 ==<br />
'''Donny'''<br />
I'm awesome</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/NotebookTeam:Illinois-Tools/Notebook2009-07-02T20:51:09Z<p>Damfahr2: </p>
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week1 5/24-5/30]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week2 5/31-6/6]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week3 6/7-6/13]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week4 6/14-6/20]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week5 6/21-6/27]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week6 6/28-7/4]</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week6Team:Illinois-Tools/Notebook/Week62009-07-02T20:50:16Z<p>Damfahr2: New page: :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week5 <<previous week] [https://2009.igem.org/Team:Illinois-...</p>
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== 6/28-7/4 ==</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week5Team:Illinois-Tools/Notebook/Week52009-07-02T20:49:39Z<p>Damfahr2: New page: :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week4 <<previous week] [https://2009.igem.org/Team:Illinois-...</p>
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== 6/21-6/27 ==</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/NotebookTeam:Illinois-Tools/Notebook2009-06-19T18:53:46Z<p>Damfahr2: </p>
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!align="center"|[[Team:Illinois-Tools|Home]]<br />
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!align="center"|[[Team:Illinois-Tools/ResearchArticles|Research Articles]]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week1 5/24-5/30]<br />
<br />
[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week2 5/31-6/6]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week3 6/7-6/13]<br />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week4 6/14-6/20]</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week4Team:Illinois-Tools/Notebook/Week42009-06-19T18:53:22Z<p>Damfahr2: </p>
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<br />
== 6/14-6/20 ==<br />
<br />
<br />
'''Donny'''<br />
<br />
I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palek found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production. <br />
<br />
In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week3Team:Illinois-Tools/Notebook/Week32009-06-19T18:52:43Z<p>Damfahr2: </p>
<hr />
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[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week2 <<previous week] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week4 next week>>]<br />
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<br />
== 6/7-6/13 ==<br />
<br />
<br />
'''Donny'''<br />
<br />
We have considered using toxic chemicals as inputs to our program to suggest a pathway that would convert harmful pollutants into valuable chemicals. I wrote a script that scans a list of harmful chemicals from the EPA and then forms a dictionary pairing the chemical name to its KEGG_ID. The script doesn't quite work perfectly and not all chemicals are found on Kegg. This will be improved throughout the week. Also, I am looking into the possibility of using django to host our application on the web.<br />
<br />
I was finally able to figure out who that girl is that I saw in the gatehouse and at work. Potential suspects were Lucy from the other team or Jacinda the secretary. After extensive facebook searches, the unlikely candidate of Julie Richards turned out to be the culprit. I look forward to meeting her or something so I feel less strange about all the stalking<br />
<br />
'''Riyad'''<br />
Read articles related to metabolic pathways and biological networks to better understand how fluxes work. Also messed around with the Flux Balance Analysis in the COBRA toolbox.<br />
<br />
'''Kanishka'''<br />
Worked on learning the python language through tutorials and textbooks.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week2Team:Illinois-Tools/Notebook/Week22009-06-19T18:52:15Z<p>Damfahr2: </p>
<hr />
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<br />
[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week1 <<previous week] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week3 next week>>]<br />
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<br />
== 5/31-6/6 ==<br />
<br />
<br />
'''Donny'''<br />
<br />
This week, I learned the basics of the python programming language. I spend most of my time working with the Kegg API to access data via the SOAP protocol. I was able to utilize this new information to create a module that converts the common name to a usable kegg_id and also to convert the kegg_id back to a name. One concern I have is that even these simple functions are somewhat slow. Perhaps we will find ways to speed these processes up in the weeks to come. I looked into the possibility of Google App Engine. The one shortcoming (although it is pretty cool) was that there were some restrictions as to which libraries can be used. I foresee this as a problem and am looking into other options. <br />
<br />
'''Riyad'''<br />
<br />
We got Cobra working so I spent the majority of the week getting used to how Python and Cobra worked.<br />
<br />
'''Palak'''<br />
<br />
I began working with the various functions in COBRA. I spent a lot of time understanding the output of COBRA and determining what aspects are necessary in creating an optimal pathway. I also looked at the inputs required for various COBRA functions and looked into ways that we can pass information from the KEGG database into COBRA. Additionally, I spend some time looking at the COBRA source code to see what we could modify to fit the needs of our program.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week1Team:Illinois-Tools/Notebook/Week12009-06-19T18:51:49Z<p>Damfahr2: </p>
<hr />
<div>[https://2009.igem.org/Team:Illinois-Tools/Notebook <<back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week2 next week>>]<br />
<br />
<br />
== 5/24-5/30 ==<br />
<br />
<br />
The team developed a better idea of how we are to make this software thanks to the advice and guidance from Professor Bhalerao.<br />
<br />
'''Donny'''<br />
<br />
I spent the week brainstorming possible ideas and applications of our project as well as researching some of the considerations we might need to account for. I also looked into what software tools have been made in the past to ensure originality of our design. We made a list of "Donny's Crazy Ideas" for the project. After a lot of brainstorming, we decided to stick with our original idea after all, but the planning process was very beneficial because it gave some direction on how to get started. <br />
<br />
Im not sure what Nate thinks he will get by sucking up to me, but I don't trust him for a second. <br />
<br />
'''Nate'''<br />
<br />
Nate learned some fun basic stuff about Python. Also, he looked into graphical options that we hope to use in the future in conjunction with our program with help from Kanishka. Graphviz was the main application investigated, as well as the modules that would be needed to run it via Python, such as Pydot, Pygraphviz, and Networkx. Not sure what Donny is talking about, given that the software has yet to be written. However, he is very thankful to have Donny "The Ultimate Programmer" Amfahr on the team for his infinite knowledge and wisdom about programming and such.<br />
<br />
'''Palak'''<br />
<br />
I read papers by Dr. Price about constraint based modeling and the factors that need to be taken into account when genome-scale models are created. I read another paper that described a program call COBRA that is used for constraint based modeling. I also began learning how to program in python.</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week4Team:Illinois-Tools/Notebook/Week42009-06-19T18:50:48Z<p>Damfahr2: </p>
<hr />
<div>:[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook]<br />
<br />
[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week3 <<previous week] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week5 next week>>]<br />
<br />
'''Donny'''<br />
<br />
I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palek found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production. <br />
<br />
In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week4Team:Illinois-Tools/Notebook/Week42009-06-19T18:40:41Z<p>Damfahr2: </p>
<hr />
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<br />
[https://2009.igem.org/Team:Illinois-Tools/Notebook/Week3 <<previous week] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week5 next week>>]<br />
<br />
'''Donny'''<br />
Sweet</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week4Team:Illinois-Tools/Notebook/Week42009-06-19T18:38:29Z<p>Damfahr2: New page: :[https://2009.igem.org/Team:Illinois-Tools/Notebook back to notebook] [https://2009.igem.org/Team:Illinois-Tools/Notebook/Week4 <<previous week] [https://2009.igem.org/Team:Illinois-...</p>
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'''Donny'''<br />
Sweet</div>Damfahr2http://2009.igem.org/Team:Illinois-ToolsTeam:Illinois-Tools2009-06-12T16:45:56Z<p>Damfahr2: </p>
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We are the 2009 University of Illinois Tools Track Team; <br> project description and more to be added!<br />
[[Image:A37cw3.jpg | 250 px | center]]<br />
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{|align="justify"<br />
|This is the first software tools team from Illinois (Not the backstreet boys). We are comprised of Biology, Bioengineering, and Chemical Engineering majors. With limited programming and synthetic biology experience we have been learning a lot along the way. Our wiki is a total joke but Nate will make it awesome in the near-future. <br />
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Our tool will utilize the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. We will most likely create a list of toxic pollutants as our input to the pathway and have value added products such as biofuels as the product. The goal is to create a network of reactions that connect our input to output and then to determine an optimal path. We are going to focus this task on one or two hosts (most likely E. Coli or Yeast). Constraint based reconstruction analysis (COBRA) will be used to determine the production rates of our product. The goal is to hopefully link together reactions in such a way that production and biomass growth are working together (thus it is favorable for the host to be producing). Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures. <br />
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This product description should be updated. <br />
|[[Image:teampic.jpg | 250 px]]<br />
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|align="center"|[[Team:Illinois-Tools | Team Example]]<br />
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<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Illinois-Tools|Home]]<br />
!align="center"|[[Team:Illinois-Tools/Team|The Team]]<br />
!align="center"|[[Team:Illinois-Tools/Project|The Project]]<br />
!align="center"|[[Team:Illinois-Tools/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Illinois-Tools/Modeling|Modeling]]<br />
!align="center"|[[Team:Illinois-Tools/ResearchArticles|Research Articles]]<br />
!align="center"|[[Team:Illinois-Tools/Notebook|Notebook]]<br />
|}<br />
(''Or you can choose different headings. But you must have a team page, a project page, and a notebook page.'')<br />
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{{CURRENTVERSION}}</div>Damfahr2http://2009.igem.org/Team:Illinois-ToolsTeam:Illinois-Tools2009-06-12T16:45:29Z<p>Damfahr2: </p>
<hr />
<div><div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: orange;"><br />
<div style="text-align:center; font-weight:bold; font-size:large; color: blue;"><br />
We are the 2009 University of Illinois Tools Track Team; <br> project description and more to be added!<br />
[[Image:A37cw3.jpg | 500 px | center]]<br />
</div><br />
</div><br />
<br />
{|align="justify"<br />
|This is the first software tools team from Illinois (Not the backstreet boys). We are comprised of Biology, Bioengineering, and Chemical Engineering majors. With limited programming and synthetic biology experience we have been learning a lot along the way. Our wiki is a total joke but Nate will make it awesome in the near-future. <br />
<br />
|-<br />
|<br />
Our tool will utilize the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. We will most likely create a list of toxic pollutants as our input to the pathway and have value added products such as biofuels as the product. The goal is to create a network of reactions that connect our input to output and then to determine an optimal path. We are going to focus this task on one or two hosts (most likely E. Coli or Yeast). Constraint based reconstruction analysis (COBRA) will be used to determine the production rates of our product. The goal is to hopefully link together reactions in such a way that production and biomass growth are working together (thus it is favorable for the host to be producing). Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures. <br />
<br />
This product description should be updated. <br />
|[[Image:teampic.jpg | 250 px]]<br />
|-<br />
|<br />
|align="center"|[[Team:Illinois-Tools | Team Example]]<br />
|}<br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Illinois-Tools|Home]]<br />
!align="center"|[[Team:Illinois-Tools/Team|The Team]]<br />
!align="center"|[[Team:Illinois-Tools/Project|The Project]]<br />
!align="center"|[[Team:Illinois-Tools/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Illinois-Tools/Modeling|Modeling]]<br />
!align="center"|[[Team:Illinois-Tools/ResearchArticles|Research Articles]]<br />
!align="center"|[[Team:Illinois-Tools/Notebook|Notebook]]<br />
|}<br />
(''Or you can choose different headings. But you must have a team page, a project page, and a notebook page.'')<br />
<br />
{{CURRENTVERSION}}</div>Damfahr2http://2009.igem.org/Team:Illinois-Tools/Notebook/Week3Team:Illinois-Tools/Notebook/Week32009-06-10T21:40:35Z<p>Damfahr2: </p>
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'''Donny'''<br />
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We have considered using toxic chemicals as inputs to our program to suggest a pathway that would convert harmful pollutants into valuable chemicals. I wrote a script that scans a list of harmful chemicals from the EPA and then forms a dictionary pairing the chemical name to its KEGG_ID. The script doesn't quite work perfectly and not all chemicals are found on Kegg. This will be improved throughout the week. Also, I am looking into the possibility of using django to host our application on the web.<br />
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I was finally able to figure out who that girl is that I saw in the gatehouse and at work. Potential suspects were Lucy from the other team or Jacinda the secretary. After extensive facebook searches, the unlikely candidate of Julie Richards turned out to be the culprit. I look forward to meeting her or something so I feel less strange about all the stalking</div>Damfahr2