1. MuPIT Interactive - Programmatic Link to MuPIT Exercise: Find a protein structure and its amino residue where the genomic location chr17:7577115 maps to, without using MuPIT’s “Query Your Mutation” panel.

2. On a web browser, go to http://mupit.icm.jhu.edu?gm=chr17:7577115 MuPIT Interactive - Programmatic Link to MuPIT Exercise: Find a protein structure and its amino residue where the genomic location chr17:7577115 maps to, without using MuPIT’s “Query Your Mutation” panel.

3. MuPIT Interactive - Programmatic Link to MuPIT Exercise: Find a protein structure and its amino residue where the genomic location chr17:7577115 maps to, without using MuPIT’s “Query Your Mutation” panel.

4. The format of query URL is http://mupit.icm.jhu.edu?gm=chromosome:position MuPIT Interactive - Programmatic Link to MuPIT Exercise: Find a protein structure and its amino residue where the genomic location chr17:7577115 maps to, without using MuPIT’s “Query Your Mutation” panel. Not all genomic locations will have a protein location mapping.

5. The format of query URL is http://mupit.icm.jhu.edu?gene=gene-name MuPIT Interactive - Programmatic Link to MuPIT Exercise: Open MuPIT with a gene name.

6. MuPIT Interactive - Programmatic Link to MuPIT Exercise: Make an HTML page with an embedded link to MuPIT. Write an HTML page which has a link to MuPIT. Clicking the link should open a new browser window or tab with MuPIT, showing the genomic to protein location mapping for chr10:123279680.

7. MuPIT Interactive- Programmatic Link to MuPIT Exercise: Make an HTML page with an embedded link to MuPIT. Click here to open a MuPIT Interactive page for chr10:123279680!http://mupit.icm.jhu.edu?gm=chr10:123279680 Write an HTML page which has a link to MuPIT. Clicking the link should open a new browser window or tab with MuPIT, showing the genomic to protein location mapping for chr10:123279680.

8. MuPIT Interactive- Programmatic Link to MuPIT Exercise: Make an HTML page with an embedded link to MuPIT.

9. MuPIT Interactive- Programmatic Link to MuPIT Exercise: Make an HTML page with an embedded link to MuPIT.

10. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation (http://training.cravat.us/rest/service/query?mutation=chr22_30421786_+_A_T) CRAVAT Browser Query as URL Result as JSON {"Chromosome":"chr22","Position":"30421786","Strand":"+","Reference base":"A","Alternate base":"T","HUGO symbol":"MTMR3","Reference transcript (priority to coding change)":"NM_021090.3","Reference transcript strand":"+","Reference transcript codon change":"aAc>aTc","Reference transcript amino acid position":"1198","Reference transcript sequence Ontology":"MS","Reference transcript reference amino acid(s)":"N","Reference transcript protein sequence change":"I","Other transcripts":"NM_153051.2:aAc>aTc:N1161I|1161, NM_153050.2:aAc>aTc:N1170I|1170, ENST00000323630:aAc>aTc:N1062I|1062, ENST00000351488:aAc>aTc:N1161I|1161, ENST00000333027:aAc>aTc:N1170I|1170, ENST00000406629:aAc>aTc:N1170I|1170, ENST00000401950:aAc>aTc:N1198I|1198","ExAC total allele frequency":"0.0021585500799119472503662109375","ExAC allele frequency (African/African American)":"0.0238370001316070556640625","ExAC allele frequency (Latino)":"0.001123600057326257228851318359375","ExAC allele frequency (East Asian)":"0","ExAC allele frequency (Finnish)":"0","ExAC allele frequency (Non-Finnish European)":"0","ExAC allele frequency (Other)":"0.0011037499643862247467041015625","ExAC allele frequency (South Asian)":"0","1000 Genomes allele frequency":"0.0077875400893390178680419921875","ESP6500 allele frequency (European American)":"0","ESP6500 allele frequency (African American)":"0.02269629947841167449951171875","Transcript in COSMIC":"","Protein sequence change in COSMIC":"","Occurrences in COSMIC [exact nucleotide change]":"","Occurrences in COSMIC by primary sites [exact nucleotide change]":""}

11. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Exercise: Single-Mutation Query with CRAVAT WebAPI

12. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Exercise: Single-Mutation Query with CRAVAT WebAPI URL: http://training.cravat.us/rest/service/query?mutation= chromosome_position_strand_reference-bases_alternate-bases

13. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Exercise: Single-Mutation Query with CRAVAT WebAPI URL: http://training.cravat.us/rest/service/query?mutation= chromosome_position_strand_reference-bases_alternate-bases Get CRAVAT annotation output in JSON format for the mutation A to T on the plus strand of chromosome 22 at position 30421786.

14. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Exercise: Single-Mutation Query with CRAVAT WebAPI URL: http://training.cravat.us/rest/service/query?mutation= chromosome_position_strand_reference-bases_alternate-bases Get CRAVAT annotation output in JSON format for the mutation A to T on the plus strand of chromosome 22 at position 30421786. Use the following URL on a web browser. http://training.cravat.us/rest/service/query?mutation=chr22_30421786_+_A_T

15. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Exercise: Single-Mutation Query with CRAVAT WebAPI

16. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation "Chromosome":"chr22“ "Position":"30421786“ "Strand":"+“ "Reference base":"A“ "Alternate base":"T“ "HUGO symbol":"MTMR3“ "Reference transcript (priority to coding change)":"NM_021090.3“ "Reference transcript strand":"+“ "Reference transcript codon change":"aAc>aTc“ "Reference transcript amino acid position":"1198“ "Reference transcript sequence Ontology":"MS“ "Reference transcript reference amino acid(s)":"N“ "Reference transcript protein sequence change":"I“ "Other transcripts":"NM_153051.2:aAc>aTc:N1161I|1161, NM_153050.2:aAc>aTc:N1170I|1170, ENST00000323630:aAc>aTc:N1062I|1062, ENST00000351488:aAc>aTc:N1161I|1161, ENST00000333027:aAc>aTc:N1170I|1170, ENST00000406629:aAc>aTc:N1170I|1170, ENST00000401950:aAc>aTc:N1198I|1198“ "ExAC total allele frequency":"0.0021585500799119472503662109375“ "ExAC allele frequency (African/African American)":"0.0238370001316070556640625“ "ExAC allele frequency (Latino)":"0.001123600057326257228851318359375“ "ExAC allele frequency (East Asian)":"0","ExAC allele frequency (Finnish)":"0“ "ExAC allele frequency (Non-Finnish European)":"0“ "ExAC allele frequency (Other)":"0.0011037499643862247467041015625“ "ExAC allele frequency (South Asian)":"0“ "1000 Genomes allele frequency":"0.0077875400893390178680419921875“ "ESP6500 allele frequency (European American)":"0“ "ESP6500 allele frequency (African American)":"0.02269629947841167449951171875“ "Transcript in COSMIC":"","Protein sequence change in COSMIC":"“ "Occurrences in COSMIC [exact nucleotide change]":"“ "Occurrences in COSMIC by primary sites [exact nucleotide change]":"" Exercise: Single-Mutation Query with CRAVAT WebAPI

17. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Extra Credit: Use CRAVAT WebAPI with a Program Write a program (of the language of your choice) that queries CRAVAT WebAPI for the 1000 Genomes allele frequency of the mutation A to T on the plus strand of chromosome 22 at position 30421786.

18. CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Extra Credit: Use CRAVAT WebAPI with a Program Write a program (of the language of your choice) that queries CRAVAT WebAPI for the 1000 Genomes allele frequency of the mutation A to T on the plus strand of chromosome 22 at position 30421786. Python example >import requests >r = requests.get(‘http://training.cravat.us/rest/service/query?mutation=chr22_30421786_+_A_T’) >output = r.json() >af = float(output[‘1000 Genomes allele frequency’]) >af 0.007787540089339018 If you don’t have Python “requests” module, try on the command line >pip install requests Or, follow the instruction on http://docs.python-requests.org/en/latest/user/install/.http://docs.python-requests.org/en/latest/user/install/

19. >output {u'Transcript in COSMIC': u'', u'Reference transcript (priority to coding change)': u'NM_021090.3', u'Reference transcript protein sequence change': u'I', u'ExAC total allele frequency': u'0.0021585500799119472503662109375', u'ExAC allele frequency (African/African American)': u'0.0238370001316070556640625', u'Reference transcript amino acid position': u'1198', u'Reference transcript strand': u'+', u'ExAC allele frequency (Non-Finnish European)': u'0', u'ExAC allele frequency (South Asian)': u'0', u'Alternate base': u'T', u'HUGO symbol': u'MTMR3', u'1000 Genomes allele frequency': u'0.0077875400893390178680419921875', u'ExAC allele frequency (Other)': u'0.0011037499643862247467041015625', u'Occurrences in COSMIC by primary sites [exact nucleotide change]': u'', u'ESP6500 allele frequency (African American)': u'0.02269629947841167449951171875', u'Position': u'30421786', u'Reference base': u'A', u'Reference transcript codon change': u'aAc>aTc', u'Protein sequence change in COSMIC': u'', u'ExAC allele frequency (East Asian)': u'0', u'ExAC allele frequency (Finnish)': u'0', u'Other transcripts': u'NM_153051.2:aAc>aTc:N1161I|1161, NM_153050.2:aAc>aTc:N1170I|1170, ENST00000323630:aAc>aTc:N1062I|1062, ENST00000351488:aAc>aTc:N1161I|1161, ENST00000333027:aAc>aTc:N1170I|1170, ENST00000406629:aAc>aTc:N1170I|1170, ENST00000401950:aAc>aTc:N1198I|1198', u'Reference transcript sequence Ontology': u'MS', u'Occurrences in COSMIC [exact nucleotide change]': u'', u'Reference transcript reference amino acid(s)': u'N', u'ESP6500 allele frequency (European American)': u'0', u'Strand': u'+', u'ExAC allele frequency (Latino)': u'0.001123600057326257228851318359375', u'Chromosome': u'chr22'} CRAVAT WebAPI for Single Mutation Fast, URL-Based Query for One Mutation Extra Credit: Use CRAVAT WebAPI with a Program Write a program (of the language of your choice) that queries CRAVAT WebAPI for the 1000 Genomes allele frequency of the mutation A to T on the plus strand of chromosome 22 at position 30421786.

20. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission of a job via HTTP GET or POST Result will be emailed just as with a web browser-based submission.

21. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission of a job via HTTP GET or POST Result will be emailed just as with a web browser-based submission. WebAPI URL: http://training.cravat.us/rest/service/submithttp://training.cravat.us/rest/service/submit

22. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission of a job via HTTP GET or POST Result will be emailed just as with a web browser-based submission. WebAPI URL: http://training.cravat.us/rest/service/submithttp://training.cravat.us/rest/service/submit For the details of the job submission WebAPI, see Help > How to Use > Web Service at http://training.cravat.us.http://training.cravat.us

23. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission via HTTP GET Submission pararmeters in the URL analyses: "CHASM", "SnvGet", "VEST", "CHASM;SnvGet", or "VEST;SnvGet" chasmclassifier: classifier name for CHASM analysis email: email of the submitter hg18: "on" or "off". Input mutations are in hg18 coordinates or not. mutations: a string with mutations. Use “%2B” instead of “+”. tsvreport: "on" or "off". Text format reports returned or not. Return value as JSON status: "submitted" for successful job submission, "submissonfailed" for an error in the job submission errormsg: If there was any error during the job submission, the error message is written here. jobid: The Job ID of the submitted job. This job ID can be used to check the status of the job later using "status" method which is explained below. >import requests >r = requests.get('http://training.cravat.us/rest/service/submit?mutations=1%20chr22 %2030421786 %2B A T&chasmclassifier=Ovary&email=rkim@insilico.us.com&tsvreport=on') >output = r.json() >output[‘status’] u’submitted’

24. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission via HTTP POST Submission pararmeters as dictionaries analyses: "CHASM", "SnvGet", "VEST", "CHASM;SnvGet", or "VEST;SnvGet" chasmclassifier: classifier name for CHASM analysis email: email of the submitter hg18: "on" or "off". Input mutations are in hg18 coordinates or not. inputfile: Input mutation file tsvreport: "on" or "off". Text format reports returned or not. Return value as JSON status: "submitted" for successful job submission, "submissonfailed" for an error in the job submission errormsg: If there was any error during the job submission, the error message is written here. jobid: The Job ID of the submitted job. This job ID can be used to check the status of the job later using "status" method which is explained below. >import requests >r = requests.post('http://training.cravat.us/rest/service/submit', files={'inputfile':('input.txt', open('c:\\input.txt', 'r'))}, data={'chasmclassifier':'Ovary', 'email':'rkim@insilico.us.com‘, ‘tsvreport’:’on’}) >output = r.json() >output[‘status’] u’submitted’

25. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Submission via HTTP POST Submission pararmeters as dictionaries analyses: "CHASM", "SnvGet", "VEST", "CHASM;SnvGet", or "VEST;SnvGet" chasmclassifier: classifier name for CHASM analysis email: email of the submitter hg18: "on" or "off". Input mutations are in hg18 coordinates or not. inputfile: Input mutation file tsvreport: "on" or "off". Text format reports returned or not. Return value as JSON status: "submitted" for successful job submission, "submissonfailed" for an error in the job submission errormsg: If there was any error during the job submission, the error message is written here. jobid: The Job ID of the submitted job. This job ID can be used to check the status of the job later using "status" method which is explained below. >import requests >r = requests.post('http://training.cravat.us/rest/service/submit', files={'inputfile':('input.txt', open('c:\\input.txt', 'r'))}, data={'chasmclassifier':'Ovary', 'email':'rkim@insilico.us.com‘, ‘tsvreport’:’on’}) >output = r.json() >output[‘status’] u’submitted’ input.txt V1 chr22 30421786 + A T

26. CRAVAT WebAPI for Job Submission Programmatic Submission of CRAVAT Jobs Checking Job Status URL: http://training.cravat.us/rest/service/statushttp://training.cravat.us/rest/service/status Method: GET Query parameters: jobid: The job ID to query. Produces: a JSON object, notable fields of which are as follows. status: "running" for still running, "completed" for successful completion, "jobfailed" for failed errormsg: Error message if the job failed. resultfileurl: If the job completed successfully, the URL of the result file. >import requests >r = requests.get('http://www.cravat.us/rest/service/status?jobid=test@20140204_102423’) >output = r.json() >output[‘status’] u’running’ Retrieving Job Result URL Format: http://training.cravat.us/results/JOBID/JOBID.ziphttp://training.cravat.us/results/JOBID/JOBID.zip Example: http://training.cravat.us/results/rkim_20150319_104321/rkim_20150319_104321.ziphttp://training.cravat.us/results/rkim_20150319_104321/rkim_20150319_104321.zip

27. Thank You