Difference between revisions of "Cipher cracking 2019 weekly progress"

Revision as of 19:42, 11 November 2019 (view source) A1684198 (Talk | contribs) (→‎Zihe (Peter)) ← Older edit		Latest revision as of 19:54, 11 November 2019 (view source) A1684198 (Talk | contribs) (→‎Semester 1 Week 11)
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	#* Completed kit order from 23andMe		#* Completed kit order from 23andMe
	# Goals for week 4:		# Goals for week 4:
		+	#* Meet with Derek for further instructions
	====Zihe (Peter)====		====Zihe (Peter)====
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	# Goals for week 4:		# Goals for week 4:
		+	#* Meet with Derek for further instructions
	=== Semester 1 Week 4===		=== Semester 1 Week 4===
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	#* Meeting with Derek		#* Meeting with Derek
	# Goals for week 5:		# Goals for week 5:
−	#*	+	#*Present the outcomes and discuss further tasks with Derek
	====Zihe (Peter)====		====Zihe (Peter)====
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	#*Also use the homozygous pairs to fill in the blanks SNPs		#*Also use the homozygous pairs to fill in the blanks SNPs
	# Goals for week 5:		# Goals for week 5:
−	#*	+	#*Present the outcomes and discuss further tasks with Derek
	=== Semester 1 Week 5===		=== Semester 1 Week 5===
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	#* Meeting with Peter to discuss about the presentation for proposal seminar		#* Meeting with Peter to discuss about the presentation for proposal seminar
	# Goals for week 6:		# Goals for week 6:
−	#*	+	#*Complete and submit the seminar slides
	====Zihe (Peter)====		====Zihe (Peter)====
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	#* Completed the slides together with Peter		#* Completed the slides together with Peter
	# Goals for week 7:		# Goals for week 7:
−	#*	+	#*Wait for the DNA samples and start degradation tasks
	====Zihe (Peter)====		====Zihe (Peter)====
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	#* Finished the slides presentation and submitted to MyUni		#* Finished the slides presentation and submitted to MyUni
	# Goals for week 7:		# Goals for week 7:
−	#*	+	#*Wait for the DNA samples and start degradation tasks
	=== Semester 1 Week 7===		=== Semester 1 Week 7===
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	#* Meeting with Derek and Peter		#* Meeting with Derek and Peter
	# Goals for week 8:		# Goals for week 8:
−	#*	+	#*Start researching on what information in dbSNP can be collected
	====Zihe (Peter)====		====Zihe (Peter)====
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	====Azizul====		====Azizul====
	# Week 8 work done:		# Week 8 work done:
−	#*	+	#* Provide a list of variables or information for Peter's data mining program to capture
	# Goals for week 9 and mid-break:		# Goals for week 9 and mid-break:
−	#*	+	#*Developing program for degrading sample DNA reference file to Somerton Man's level
	====Zihe (Peter)====		====Zihe (Peter)====
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	====Azizul====		====Azizul====
	# Week 9 and mid break work done:		# Week 9 and mid break work done:
−	#*	+	#* Searching on genetic diseases associated with SNPs has done
	# Goals for week 10:		# Goals for week 10:
−	#*	+	#*Investigate any genetic diseases in the list is relevant to Somerton Man's characteristics
	====Zihe (Peter)====		====Zihe (Peter)====
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	====Azizul====		====Azizul====
	# Week 10 work done:		# Week 10 work done:
−	#*	+	#* Investigation on genetic diseases done, no results relevant to known characteristics
	# Goals for week 11:		# Goals for week 11:
−	#*	+	#* Investigate the genetic diseases in the outcomes of new data mining program
	====Zihe (Peter)====		====Zihe (Peter)====
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	====Azizul====		====Azizul====
	# Week 11 work done:		# Week 11 work done:
−	#*	+	#* Investigation on new genetic diseases list done, no results relevant to known characteristics
	# Goals for week 12:		# Goals for week 12:
−	#*	+	#*Working on draft thesis
	====Zihe (Peter)====		====Zihe (Peter)====
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	====Azizul====		====Azizul====
	# Week 12 work done:		# Week 12 work done:
−	#*	+	#* Finish the draft thesis
	# Goals for Week 13:		# Goals for Week 13:
−	#*	+	#*Meet with Derek to discuss tasks for mid break
	====Zihe (Peter)====		====Zihe (Peter)====
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	# Goals for Week 13:		# Goals for Week 13:
	#*Meet with Derek to discuss tasks for mid break		#*Meet with Derek to discuss tasks for mid break
		+
	=== Semester 1 Week 12===		=== Semester 1 Week 12===

---

Latest revision as of 19:54, 11 November 2019

Weekly progress and questions

This is where you record your progress and ask questions. Make sure you update this every week. The deadline is every Friday evening. However, if you sometimes slip a little into the weekend (so long as you don't do it too often) we won't be too hard on your marks.

Please remember that we make use of this progress section to give you your project mark. Your mark will suffer if you don't complete this section.

Semester 1 Week 1

Azizul

1. Week 1 work done:
   • Researched about the Somerton Man case
   • Attend project briefing with Hong Gunn
   • First meeting with Zihe Wang
   • Planned a meeting with Derek
2. Goals for week 2:
   • Initiate a meeting with Prof. Derek Abbott
   • Understand what the project is about

Zihe (Peter)

1. Week 1 work done:
   • Met project partner Azizul.
   • Planned a meeting with Derek Abbott.
   • Research on the Somerton Man's case.
     • A little reading at https://www.abc.net.au/news/2018-12-01/will-the-mystery-of-the-somerton-man-ever-be-solved/10420794
2. Goals for week 2:
   • Meeting with Derek.
   • Get to know more detail about the project.

Semester 1 Week 2

Azizul

1. Week 2 work done:
   • Attended a briefing from the lab support manager, Andrew Heathershaw
   • Meeting with Derek and Zihe
   • Briefing about bioinformatics engineering
     • DNAs, rsid, chromosomes
   • Introduction to the project wiki
     • Created 2019 wiki
     • Started exploring wiki and details of previous work done by previous students
2. Goals for week 3:
   • Start requesting for fund provided by uni to get the kit from 23andme website (https://www.23andme.com/en-int/)

Zihe (Peter)

1. Week 2 work done:
   • Briefing from the lab support manager, Andrew Heathershaw
   • Meeting with project members Derek and Azizul
   • Details about the overall project, explained by Derek
2. Goals for week 3:
   • Count the data in the given data file by Derek

Semester 1 Week 3

Azizul

1. Week 3 work done:
   • Requested fund from the School of Electrical and Electronic Engineering to purchase the kit from 23andme
   • Completed kit order from 23andMe
2. Goals for week 4:
   • Meet with Derek for further instructions

Zihe (Peter)

1. Week 3 work done:
   • Counted the number of SNP for each chromosome using C++ and excel

1. Goals for week 4:
   • Meet with Derek for further instructions

Semester 1 Week 4

Azizul

1. Week 4 work done:
   • Meeting with Derek
2. Goals for week 5:
   • Present the outcomes and discuss further tasks with Derek

Zihe (Peter)

1. Week 4 work done:
   • Completed generating random SNP to fill in the blanks in Somerton man's DNA file
   • Also use the homozygous pairs to fill in the blanks SNPs
2. Goals for week 5:
   • Present the outcomes and discuss further tasks with Derek

Semester 1 Week 5

Azizul

1. Week 5 work done:
   • Meeting with Peter to discuss about the presentation for proposal seminar
2. Goals for week 6:
   • Complete and submit the seminar slides

Zihe (Peter)

1. Week 5 work done:
   • Meeting with Azizul regarding proposal seminar presentation
2. Goals for week 6:
   • Complete and submit the seminar slides

Semester 1 Week 6

Azizul

1. Week 6 work done:
   • Received package (saliva collection kit) from 23andme
   • Returned the packages to 23andme to extract DNA data
   • Meeting with Derek and Peter to discuss about slides presentation
   • Completed the slides together with Peter
2. Goals for week 7:
   • Wait for the DNA samples and start degradation tasks

Zihe (Peter)

1. Week 6 work done:
   • Meeting with Azizul and Derek to discuss about slides
   • Meeting with Azizul to adjust slides for proposal seminar
   • Finished the slides presentation and submitted to MyUni
2. Goals for week 7:
   • Wait for the DNA samples and start degradation tasks

Semester 1 Week 7

Azizul

1. Week 7 work done:
   • Meeting with Derek and Peter
2. Goals for week 8:
   • Start researching on what information in dbSNP can be collected

Zihe (Peter)

1. Week 7 work done:
   • Received DNA data from 23andme
   • Began uploading data to GedMatch Genesis
2. Goals for week 8:
   • Developing data mining program for genetic diseases

Semester 1 Week 8

Azizul

1. Week 8 work done:
   • Provide a list of variables or information for Peter's data mining program to capture
2. Goals for week 9 and mid-break:
   • Developing program for degrading sample DNA reference file to Somerton Man's level

Zihe (Peter)

1. Week 8 work done:
   • Work on genetic diseases associated with SNPs nearly done
2. Goals for week 9 and mid-break:
   • Developing program for degrading sample DNA reference file to Somerton Man's level

Semester 1 Week 9

Azizul

1. Week 9 and mid break work done:
   • Searching on genetic diseases associated with SNPs has done
2. Goals for week 10:
   • Investigate any genetic diseases in the list is relevant to Somerton Man's characteristics

Zihe (Peter)

1. Week 9 and mid break work done:
   • Searching on genetic diseases associated with SNPs has done
   • A list of genetic diseases is provided
   • Complete DNA sample 1 degraded and upload to GEDmatch
2. Goals for week 10:
   • Investigate any genetic diseases in the list is relevant to Somerton Man's characteristics

Semester 1 Week 10

Azizul

1. Week 10 work done:
   • Investigation on genetic diseases done, no results relevant to known characteristics
2. Goals for week 11:
   • Investigate the genetic diseases in the outcomes of new data mining program

Zihe (Peter)

1. Week 10 work done:
   • Investigation on genetic diseases done, no results relevant to known characteristics
2. Goals for week 11:
   • Modify the data mining program so that it only searched with non empty SNPs

Semester 1 Week 11

Azizul

1. Week 11 work done:
   • Investigation on new genetic diseases list done, no results relevant to known characteristics
2. Goals for week 12:
   • Working on draft thesis

Zihe (Peter)

1. Week 11 work done:
   • Modification on the data mining program has done, it only searched with non empty SNPs
   • Searching works for new data mining program has done.
   • A new list for genetic diseases has now provided
2. Goals for week 12:
   • Working on draft thesis

Semester 1 Week 12

Azizul

1. Week 12 work done:
   • Finish the draft thesis
2. Goals for Week 13:
   • Meet with Derek to discuss tasks for mid break

Zihe (Peter)

1. Week 12 work done:
   • Finish the draft thesis
2. Goals for Week 13:
   • Meet with Derek to discuss tasks for mid break

Semester 1 Week 12

Azizul

1. Week 12 work done:
   • Met with Derek to discuss tasks for mid break
2. Goals for Mid Year Break:
   • Finding new SNPs database for genetic diseases or physical characteristics searching
   • Check tools in https://isogg.org/wiki/Raw_DNA_data_tools are useful or not
   • Check tier 1 tools in GEDmatch are useful or not

Zihe (Peter)

1. Week 12 work done:
   • Met with Derek to discuss tasks for mid break
2. Goals for Mid Year Break:
   • Optimizing the outcomes of data mining program
   • Recheck the diseases in the list
   • Check tools in https://isogg.org/wiki/Raw_DNA_data_tools

Mid Year Break

Azizul

1. Mid Year Break work done:
   • Found a tool for checking eye and hair colour. Test with complete DNA sample and it works
   • Unfortunately required SNPs for using eye and hair colour examination were empty in Somerton Man's DNA
   • No useful database found
   • No needs for updating GEDmatch account to use tier 1 tools
2. Goals for Week 1:
   • Attend the interview
   • Meet with Derek for discussing further tasks

Zihe (Peter)

1. Mid Year Break work done:
   • Optimized the outputs of data mining program
   • No diseases in the data mining outcomes fits Somerton Man's known characteristics
   • Found a tool for checking chance of risk that have genetic diseases
2. Goals for Week 1:
   • Attend the interview
   • Meet with Derek for discussing further tasks

Semester 2 Week 1

Azizul

1. Week 1 work done:
   • Attend the interview
2. Goals for Week 2:
   • Study on ethnicity regions in Somerton Man's ethnicity reports

Zihe (Peter)

1. Week 1 work done:
   • Attend the interview
2. Goals for Week 2:
   • Degrading DNA sample 1 to different levels

Semester 2 Week 2

Azizul

1. Week 2 work done:
   • Finish background research on Somerton Man's major ethnicity regions
2. Goals for Week 3:
   • Conduct ethnicity examination on new updated degraded kits

Zihe (Peter)

1. Week 2 work done:
   • Finish degrading DNA sample 1 to different levels and updated them to GEDmatch
2. Goals for Week 3:
   • Waiting the delivery of DNA sample 2

Semester 2 Week 3

Azizul

1. Week 3 work done:
   • Ethnicity examination on new updated degraded kits conducted
2. Goals for Week 4:
   • Try to find new tools that can provide useful DNA analysis services
   • Wait for FASTQ file

Zihe (Peter)

1. Week 3 work done:
   • Evaluated the outcomes of website that provide chances of having genetic disease, and the results is not reliable
2. Goals for Week 4:
   • Try to find new tools that can provide useful DNA analysis services
   • Wait for FASTQ file

Semester 2 Week 4

Azizul

1. Week 4 work done:
   • Found some DNA analysis tools, but none of them provide available results on Somerton Man's DNA
2. Goals for Week 5:
   • Wait for FASTQ file

Zihe (Peter)

1. Week 4 work done:
   • Found some DNA analysis tools, but none of them provide available results on Somerton Man's DNA
2. Goals for Week 5:
   • Wait for FASTQ file
   • Wait for DNA sample 2 and start its degradation

Semester 2 Week 5

Azizul

1. Week 5 work done:
   • Conduct the ethnicity tests on recovered DNA kits for DNA sample 1
2. Goals for Week 6:
   • Wait for FASTQ file

Zihe (Peter)

1. Week 5 work done:
   • Implement recovery algorithm on degraded DNA sample 1 and generated several recovered DNA file for DNA sample 1
2. Goals for Week 6:
   • Wait for FASTQ file
   • Wait for DNA sample 2 and start its degradation

Semester 2 Week 6

Azizul

1. Week 6 work done:
   • Searching on other SNPs databases
2. Goals for Week 7:
   • Wait for FASTQ file

Zihe (Peter)

1. Week 6 work done:
   • Examining the genetic diseases of Somerton Man's DNA again
2. Goals for Week 7:
   • Wait for FASTQ file
   • Wait for DNA sample 2 and start its degradation

Semester 2 Week 7

Azizul

1. Week 7 work done:
   • Searching on other SNPs databases
   • Searching on other tools for DNA analysis
2. Goals for Week 8:
   • Wait for FASTQ file

Zihe (Peter)

1. Week 7 work done:
   • Implementing a new degradation algorithm for degradation program (Got 2 algorithms implemented now)
2. Goals for Week 8:
   • Wait for FASTQ file
   • Wait for DNA sample 2 and start its degradation

Semester 2 Week 8

Azizul

1. Week 8 work done:
   • Searching on other tools for DNA analysis
   • Examining the genetic diseases of Somerton Man's DNA again
2. Goals for Week 9 and mid break:
   • Start the ethnicity examination on each new degraded files

Zihe (Peter)

1. Week 8 work done:
   • Implementing a new degradation algorithm for degradation program (Got 3 algorithms implemented now)
2. Goals for Week 9 and mid break:
   • Record the DNA match results for each degraded files
   • Wait for DNA sample 2 and start its degradation
   • Implement a new degradation algorithm (4th algorithm)

Semester 2 Week 9

Azizul

1. Week 9 work done:
   • Made the tables and graphs for ethnicity changes vs degradation levels according to different algorithms
2. Goals for Week 10:
   • Working on thesis and poster

Zihe (Peter)

1. Week 9 work done:
   • Implemented the last degradation algorithm
   • Start working on the counting codes required by Derek
2. Goals for Week 10:
   • Working on thesis and poster
   • Finish counting codes
   • Start false positives and false negatives test on DNA matches results

Semester 2 Week 10

Azizul

1. Week 10 work done:
   • Poster updated
2. Goals for Week 11:
   • Prepare for exhibition and working on thesis

Zihe (Peter)

1. Week 10 work done:
   • Poster updated
   • Finish the counting codes
   • Finish false positives and false negatives tests
2. Goals for Week 11:
   • Prepare for exhibition and working on thesis

Semester 2 Week 11

1. Week 11 work done:
   • Working on thesis
2. Goals for Week 12:
   • Attend exhibition and working on thesis and seminar slides

Semester 2 Week 12

1. Week 12 work done:
   • Working on thesis and seminar slides
   • Take part in exhibition
2. Goals for Week 13:
   • Finish thesis and presentation in seminar

Semester 2 Week 13

1. Week 13 progress:
   • Final seminar completed
   • Final thesis submitted
   • Closed project

Back

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• Back to Derek Abbott's homepage
• Back to EEE Department page
• Back to the University of Adelaide homepage