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http://base.thep.lu.se
Lao H. Saal1,3,*, Carl Troein2,*, Johan Vallon-Christersson1,*, Sofia Gruvberger1, Björn Samuelsson2,
Åke Borg1 and Carsten Peterson2
Departments of 1Oncology and 2Theoretical Physics, Lund University, and 3MSTP, College of Physicians & Surgeons, Columbia University
B A S EB A S EBBioio A Arrayrray S Softwareoftware E Environmentnvironment
http://base.thep.lu.se http://www.onk.lu.se http://www.thep.lu.se
http://base.thep.lu.se
Original Goals
Backend Production
• Probe/Reporter Annotation• Bacterial Growth• Events & Protocols: ie Bacterial Growth,
Plasmid Extraction,PCR, etc• Gel Bands• Microtiter Plates/Parent-Daughters• Slide Information (bar codes, batches)• Print Design/Print Map• Print Batches, Print Conditions
Integrate:
http://base.thep.lu.se
Original Goals
1 7461 206 281128 890912 890912 61 911118 920513 1 26 1 0 1 2 0 0 1 0 0 11 8582 245 310808 901129 901129 59 0 0 0 0 0 0 0 0 0 1 01 7418 295 370531 890821 890821 52 0 0 0 0 0 0 0 0 0 1 01 8751 15 160426 910212 910211 75 0 0 0 0 0 0 0 0 0 1 00 10935 236 301118 931020 930920 63 961111 961111 1 36.9667 1 0 0 1 0 0 0 0 0 01 7214 288 360601 890517 890517 53 0 0 0 0 0 0 0 0 0 0 01 6616 377 501222 880803 880803 38 0 0 0 0 0 0 0 0 0 1 01 6219 47 190211 880126 880126 69 970109 1 107.833 0 0 1 1 0 0 0 0 0 10 10426 74 210122 930126 930126 72 940228 1 12.2 0 0 1 1 0 0 0 0 0 00 10879 77 210218 930830 930826 73 0 0 0 0 0 0 0 0 0 1 01 11567 85 210623 940601 940601 73 0 0 0 0 0 0 0 0 0 1 00 7495 115 230331 890914 890914 66 0 0 0 0 0 0 0 0 0 0 00 10881 126 231108 930830 930830 70 960821 1 35.3 0 0 1 1 0 0 0 0 0 10 8485 133 240106 901017 901016 67 0 0 0 0 0 0 0 0 0 0 00 8415 135 240216 900926 900926 67 0 0 0 0 0 0 0 0 0 1 01 7688 161 251029 891120 891120 64 950609 1 67.0333 0 0 1 1 0 0 0 0 0 11 7549 174 260926 891010 891010 63 0 0 0 0 0 0 0 0 0 1 01 10524 203 281103 930308 930308 64 950324 950324 1 23.9333 1 0 0 1 0 0 0 0 0 01 11078 217 290504 931110 931110 65 0 0 0 0 0 0 0 0 0 1 01 7398 267 330528 890720 890720 56 0 0 0 0 0 0 0 0 0 0 00 7246 349 440118 890524 890524 45 0 0 0 0 0 0 0 0 0 0 01 6516 359 450901 880609 880609 43 0 0 0 0 0 0 0 0 0 1 00 9795 370 490102 920406 920406 43 0 0 0 0 0 0 0 0 0 1 01 11424 166 260227 940330 940330 68 0 0 0 0 0 0 0 0 0 1 00 11570 211 290128 940530 940630 65 940919 1 3.36667 0 0 1 1 0 0 0 0 0 10 7632 259 320804 891106 891106 57 0 0 0 0 0 0 0 0 0 0 01 9077 355 450206 910610 910610 46 0 0 0 0 0 0 0 0 0 1 01 8860 242 310329 910318 910318 60 0 0 0 0 0 0 0 0 0 1 00 11620 86 210625 940615 940614 73 0 0 0 0 0 0 0 0 0 0 01 9126 38 180428 910702 910702 73 0 0 0 0 0 0 0 0 0 0 00 9732 265 330318 920319 920319 59 971111 1 68 0 0 1 1 0 0 0 0 0 10 8147 13 150709 900523 900523 75 0 0 0 0 0 0 0 0 0 1 01 7422 36 180305 890822 890822 71 900517 1 8.7 0 0 1 1 0 0 0 0 0 11 11968 83 210501 941011 941109 73 0 0 0 0 0 0 0 0 0 1 01 7106 92 211218 890320 890320 67 0 0 0 0 0 0 0 0 0 0 01 7171 95 220119 890418 890418 67 960606 1 86.2 0 0 1 1 0 0 0 0 1 11 7638 124 231004 891108 891108 66 0 0 0 0 0 0 0 0 0 1 01 7366 138 240323 890704 890704 65 0 0 0 0 0 0 0 0 0 1 00 8703 159 250724 910121 910121 65 980109 1 84 0 0 1 1 0 0 0 0 0 10 10580 202 281019 930405 930405 64 0 0 0 0 0 0 0 0 0 0 01 7589 222 290729 891030 891030 60 931001 931001 1 47.9667 1 0 0 1 0 0 0 0 0 11 9999 232 300730 920701 920701 62 0 0 0 0 0 0 0 0 0 0 01 6366 240 310115 880415 880414 57 920901 1 53.4667 0 0 1 1 0 0 0 0 1 11 7168 249 311008 890417 890417 58 0 0 0 0 0 0 0 0 0 0 00 7921 272 340305 900226 900226 56 0 0 0 0 0 0 0 0 0 0 01 7105 275 340703 890321 890321 55 0 0 0 0 0 0 0 0 0 1 01 6318 338 420405 880314 880314 46 0 0 0 0 0 0 0 0 0 0 00 7722 345 430424 891204 891204 47 0 0 0 0 0 0 0 0 0 0 00 8174 353 441007 900530 900529 46 0 0 0 0 0 0 0 0 0 0 01 6773 356 450710 881024 881025 43 0 0 0 0 0 0 0 0 0 1 01 8318 358 450831 900816 900816 45 910815 1 11.9667 0 0 1 1 0 0 0 0 0 10 7811 262 330116 900122 900122 57 0 0 0 0 0 0 0 0 0 0 00 11829 162 251102 940908 940910 69 980122 980122 1 40 1 0 0 1 0 0 0 0 0 00 11442 223 290801 940412 940412 65 0 0 0 0 0 0 0 0 0 1 00 8736 70 201117 910204 910204 70 0 0 0 0 0 0 0 0 0 0 01 6464 23 161103 880531 880531 72 0 0 0 0 0 0 0 0 0 0 00 7845 136 240317 900208 900208 66 0 0 0 0 0 0 0 0 0 0 00 9016 238 301218 910523 910523 60 970825 1 74.4 0 0 1 1 0 0 0 0 1 11 7244 252 320108 890530 890530 57 920616 1 36.4667 0 0 1 1 0 0 0 0 0 1
Backend Production
Experimental Data
+
• Raw Images• Extracted Data
Integrate:
http://base.thep.lu.se
Original Goals
1 7461 206 281128 890912 890912 61 911118 920513 1 26 1 0 1 2 0 0 1 0 0 11 8582 245 310808 901129 901129 59 0 0 0 0 0 0 0 0 0 1 01 7418 295 370531 890821 890821 52 0 0 0 0 0 0 0 0 0 1 01 8751 15 160426 910212 910211 75 0 0 0 0 0 0 0 0 0 1 00 10935 236 301118 931020 930920 63 961111 961111 1 36.9667 1 0 0 1 0 0 0 0 0 01 7214 288 360601 890517 890517 53 0 0 0 0 0 0 0 0 0 0 01 6616 377 501222 880803 880803 38 0 0 0 0 0 0 0 0 0 1 01 6219 47 190211 880126 880126 69 970109 1 107.833 0 0 1 1 0 0 0 0 0 10 10426 74 210122 930126 930126 72 940228 1 12.2 0 0 1 1 0 0 0 0 0 00 10879 77 210218 930830 930826 73 0 0 0 0 0 0 0 0 0 1 01 11567 85 210623 940601 940601 73 0 0 0 0 0 0 0 0 0 1 00 7495 115 230331 890914 890914 66 0 0 0 0 0 0 0 0 0 0 00 10881 126 231108 930830 930830 70 960821 1 35.3 0 0 1 1 0 0 0 0 0 10 8485 133 240106 901017 901016 67 0 0 0 0 0 0 0 0 0 0 00 8415 135 240216 900926 900926 67 0 0 0 0 0 0 0 0 0 1 01 7688 161 251029 891120 891120 64 950609 1 67.0333 0 0 1 1 0 0 0 0 0 11 7549 174 260926 891010 891010 63 0 0 0 0 0 0 0 0 0 1 01 10524 203 281103 930308 930308 64 950324 950324 1 23.9333 1 0 0 1 0 0 0 0 0 01 11078 217 290504 931110 931110 65 0 0 0 0 0 0 0 0 0 1 01 7398 267 330528 890720 890720 56 0 0 0 0 0 0 0 0 0 0 00 7246 349 440118 890524 890524 45 0 0 0 0 0 0 0 0 0 0 01 6516 359 450901 880609 880609 43 0 0 0 0 0 0 0 0 0 1 00 9795 370 490102 920406 920406 43 0 0 0 0 0 0 0 0 0 1 01 11424 166 260227 940330 940330 68 0 0 0 0 0 0 0 0 0 1 00 11570 211 290128 940530 940630 65 940919 1 3.36667 0 0 1 1 0 0 0 0 0 10 7632 259 320804 891106 891106 57 0 0 0 0 0 0 0 0 0 0 01 9077 355 450206 910610 910610 46 0 0 0 0 0 0 0 0 0 1 01 8860 242 310329 910318 910318 60 0 0 0 0 0 0 0 0 0 1 00 11620 86 210625 940615 940614 73 0 0 0 0 0 0 0 0 0 0 01 9126 38 180428 910702 910702 73 0 0 0 0 0 0 0 0 0 0 00 9732 265 330318 920319 920319 59 971111 1 68 0 0 1 1 0 0 0 0 0 10 8147 13 150709 900523 900523 75 0 0 0 0 0 0 0 0 0 1 01 7422 36 180305 890822 890822 71 900517 1 8.7 0 0 1 1 0 0 0 0 0 11 11968 83 210501 941011 941109 73 0 0 0 0 0 0 0 0 0 1 01 7106 92 211218 890320 890320 67 0 0 0 0 0 0 0 0 0 0 01 7171 95 220119 890418 890418 67 960606 1 86.2 0 0 1 1 0 0 0 0 1 11 7638 124 231004 891108 891108 66 0 0 0 0 0 0 0 0 0 1 01 7366 138 240323 890704 890704 65 0 0 0 0 0 0 0 0 0 1 00 8703 159 250724 910121 910121 65 980109 1 84 0 0 1 1 0 0 0 0 0 10 10580 202 281019 930405 930405 64 0 0 0 0 0 0 0 0 0 0 01 7589 222 290729 891030 891030 60 931001 931001 1 47.9667 1 0 0 1 0 0 0 0 0 11 9999 232 300730 920701 920701 62 0 0 0 0 0 0 0 0 0 0 01 6366 240 310115 880415 880414 57 920901 1 53.4667 0 0 1 1 0 0 0 0 1 11 7168 249 311008 890417 890417 58 0 0 0 0 0 0 0 0 0 0 00 7921 272 340305 900226 900226 56 0 0 0 0 0 0 0 0 0 0 01 7105 275 340703 890321 890321 55 0 0 0 0 0 0 0 0 0 1 01 6318 338 420405 880314 880314 46 0 0 0 0 0 0 0 0 0 0 00 7722 345 430424 891204 891204 47 0 0 0 0 0 0 0 0 0 0 00 8174 353 441007 900530 900529 46 0 0 0 0 0 0 0 0 0 0 01 6773 356 450710 881024 881025 43 0 0 0 0 0 0 0 0 0 1 01 8318 358 450831 900816 900816 45 910815 1 11.9667 0 0 1 1 0 0 0 0 0 10 7811 262 330116 900122 900122 57 0 0 0 0 0 0 0 0 0 0 00 11829 162 251102 940908 940910 69 980122 980122 1 40 1 0 0 1 0 0 0 0 0 00 11442 223 290801 940412 940412 65 0 0 0 0 0 0 0 0 0 1 00 8736 70 201117 910204 910204 70 0 0 0 0 0 0 0 0 0 0 01 6464 23 161103 880531 880531 72 0 0 0 0 0 0 0 0 0 0 00 7845 136 240317 900208 900208 66 0 0 0 0 0 0 0 0 0 0 00 9016 238 301218 910523 910523 60 970825 1 74.4 0 0 1 1 0 0 0 0 1 11 7244 252 320108 890530 890530 57 920616 1 36.4667 0 0 1 1 0 0 0 0 0 1
Backend Production
Experimental Data
Biological / Sample Data
+
+
• Tissue / Cell Line• Treatment / Clinical parameters• RNA Extraction / Labeling
Integrate:
http://base.thep.lu.se
Original Goals
1 7461 206 281128 890912 890912 61 911118 920513 1 26 1 0 1 2 0 0 1 0 0 11 8582 245 310808 901129 901129 59 0 0 0 0 0 0 0 0 0 1 01 7418 295 370531 890821 890821 52 0 0 0 0 0 0 0 0 0 1 01 8751 15 160426 910212 910211 75 0 0 0 0 0 0 0 0 0 1 00 10935 236 301118 931020 930920 63 961111 961111 1 36.9667 1 0 0 1 0 0 0 0 0 01 7214 288 360601 890517 890517 53 0 0 0 0 0 0 0 0 0 0 01 6616 377 501222 880803 880803 38 0 0 0 0 0 0 0 0 0 1 01 6219 47 190211 880126 880126 69 970109 1 107.833 0 0 1 1 0 0 0 0 0 10 10426 74 210122 930126 930126 72 940228 1 12.2 0 0 1 1 0 0 0 0 0 00 10879 77 210218 930830 930826 73 0 0 0 0 0 0 0 0 0 1 01 11567 85 210623 940601 940601 73 0 0 0 0 0 0 0 0 0 1 00 7495 115 230331 890914 890914 66 0 0 0 0 0 0 0 0 0 0 00 10881 126 231108 930830 930830 70 960821 1 35.3 0 0 1 1 0 0 0 0 0 10 8485 133 240106 901017 901016 67 0 0 0 0 0 0 0 0 0 0 00 8415 135 240216 900926 900926 67 0 0 0 0 0 0 0 0 0 1 01 7688 161 251029 891120 891120 64 950609 1 67.0333 0 0 1 1 0 0 0 0 0 11 7549 174 260926 891010 891010 63 0 0 0 0 0 0 0 0 0 1 01 10524 203 281103 930308 930308 64 950324 950324 1 23.9333 1 0 0 1 0 0 0 0 0 01 11078 217 290504 931110 931110 65 0 0 0 0 0 0 0 0 0 1 01 7398 267 330528 890720 890720 56 0 0 0 0 0 0 0 0 0 0 00 7246 349 440118 890524 890524 45 0 0 0 0 0 0 0 0 0 0 01 6516 359 450901 880609 880609 43 0 0 0 0 0 0 0 0 0 1 00 9795 370 490102 920406 920406 43 0 0 0 0 0 0 0 0 0 1 01 11424 166 260227 940330 940330 68 0 0 0 0 0 0 0 0 0 1 00 11570 211 290128 940530 940630 65 940919 1 3.36667 0 0 1 1 0 0 0 0 0 10 7632 259 320804 891106 891106 57 0 0 0 0 0 0 0 0 0 0 01 9077 355 450206 910610 910610 46 0 0 0 0 0 0 0 0 0 1 01 8860 242 310329 910318 910318 60 0 0 0 0 0 0 0 0 0 1 00 11620 86 210625 940615 940614 73 0 0 0 0 0 0 0 0 0 0 01 9126 38 180428 910702 910702 73 0 0 0 0 0 0 0 0 0 0 00 9732 265 330318 920319 920319 59 971111 1 68 0 0 1 1 0 0 0 0 0 10 8147 13 150709 900523 900523 75 0 0 0 0 0 0 0 0 0 1 01 7422 36 180305 890822 890822 71 900517 1 8.7 0 0 1 1 0 0 0 0 0 11 11968 83 210501 941011 941109 73 0 0 0 0 0 0 0 0 0 1 01 7106 92 211218 890320 890320 67 0 0 0 0 0 0 0 0 0 0 01 7171 95 220119 890418 890418 67 960606 1 86.2 0 0 1 1 0 0 0 0 1 11 7638 124 231004 891108 891108 66 0 0 0 0 0 0 0 0 0 1 01 7366 138 240323 890704 890704 65 0 0 0 0 0 0 0 0 0 1 00 8703 159 250724 910121 910121 65 980109 1 84 0 0 1 1 0 0 0 0 0 10 10580 202 281019 930405 930405 64 0 0 0 0 0 0 0 0 0 0 01 7589 222 290729 891030 891030 60 931001 931001 1 47.9667 1 0 0 1 0 0 0 0 0 11 9999 232 300730 920701 920701 62 0 0 0 0 0 0 0 0 0 0 01 6366 240 310115 880415 880414 57 920901 1 53.4667 0 0 1 1 0 0 0 0 1 11 7168 249 311008 890417 890417 58 0 0 0 0 0 0 0 0 0 0 00 7921 272 340305 900226 900226 56 0 0 0 0 0 0 0 0 0 0 01 7105 275 340703 890321 890321 55 0 0 0 0 0 0 0 0 0 1 01 6318 338 420405 880314 880314 46 0 0 0 0 0 0 0 0 0 0 00 7722 345 430424 891204 891204 47 0 0 0 0 0 0 0 0 0 0 00 8174 353 441007 900530 900529 46 0 0 0 0 0 0 0 0 0 0 01 6773 356 450710 881024 881025 43 0 0 0 0 0 0 0 0 0 1 01 8318 358 450831 900816 900816 45 910815 1 11.9667 0 0 1 1 0 0 0 0 0 10 7811 262 330116 900122 900122 57 0 0 0 0 0 0 0 0 0 0 00 11829 162 251102 940908 940910 69 980122 980122 1 40 1 0 0 1 0 0 0 0 0 00 11442 223 290801 940412 940412 65 0 0 0 0 0 0 0 0 0 1 00 8736 70 201117 910204 910204 70 0 0 0 0 0 0 0 0 0 0 01 6464 23 161103 880531 880531 72 0 0 0 0 0 0 0 0 0 0 00 7845 136 240317 900208 900208 66 0 0 0 0 0 0 0 0 0 0 00 9016 238 301218 910523 910523 60 970825 1 74.4 0 0 1 1 0 0 0 0 1 11 7244 252 320108 890530 890530 57 920616 1 36.4667 0 0 1 1 0 0 0 0 0 1
Backend Production
Experimental Data
Biological / Sample Data
+
+
Integrate:
Publication Server
Data Analysis
Normalization
http://base.thep.lu.se
To create a flexible and open software environment for a microarray lab (not just a database). Local database and analysis engine, not a public repository:
• Any experiment type (tumor profiling, timecourse, CGH, etc)• Any array platform (cDNA glass, nylon, Affy, etc)• Any scanner• Any normalization algorithm• Any analysis and data visualization technique• No limitation on # of experiments• Multi-user web server, individual access levels, • Hyperlinks to relevant public databases (NCBI, etc)• Very user-friendly point-and-click interface, follow natural biologist work-flow• “MIAME supportive” (MIAME++)
Extended Goals
http://base.thep.lu.se
DetailsOPEN SOURCE under GPL
Interface:• Entirely Web-accessible, user-friendly• User Accounts & defined Workspace and Projects• User-level sharing of files, projects, and data• Link to other databases (NCBI, UniGene, etc)• Secure System
Platform:• Linux Operating System• MySQL Database• Apache Webserver• PHP, C++• 1-2 Dedicated Servers
Costn/an/an/an/a
Inexpensive
http://base.thep.lu.se
Details“Plug-Ins”:
• Architecture for easy addition of your own normalizationand analysis modules to BASE
• Proof-of-concept – we wrote 2 programs and pluggedthem in:
Normalization (LOWESS, mean/median intensity)Multi-Dimensional Scaling (MDS)
Import/Export:• Import any data format using Import Wizard• Export data in standard formats (ie Eisen cluster, J-Express,
Expression Profiler, tab delimited, etc)• MAGE-ML support soon
http://base.thep.lu.se
Live Demonstration
Visit http://base.thep.lu.se for more details, screenshots,
news, contact information
http://base.thep.lu.se
Live Demonstration
ER+ ER–
Multidimensional scaling ER+luminal cell type
ER– basal cell type
http://base.thep.lu.se
Future Directions
• MAGE-ML export support (limited import)
• Beta version available to interested groups
• Public final release to academia, open source, General Public License
• Encourage other labs to write and share their own normalization/analysis plug-ins
• Write more plug-ins
• Add new features in response to user-feedback
