cgi-bin/community/snp_consortium/Labate_tomato_tech.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('Labate_tomato_tech.html','html2pl converter');
   4 $page->header('SNP Consortium Pre-proposal');
   5 print<<END_HEREDOC;
   6
   7
   8     <h2>SNP Consortium Pre-proposal</h2>
   9
  10     <p>Joanne Labate and Angela Baldo, USDA Geneva</p>
  11
  12     <p>Cultivated tomato (<em>Lycopersicon esculentum</em> var. <em>esculentum</em>
  13     is known to have relatively low molecular genetic diversity.
  14     This limited genetic variation has restricted the use of molecular
  15     markers as tools for genetic studies or crop improvement. The
  16     USDA, ARS Plant Genetic Resources Unit (PGRU) in Geneva, NY
  17     currently conserves more than 5,000 accessions of cultivated
  18     tomato. We are developing DNA sequence-based molecular markers
  19     (Single Nucleotide Polymorphisms, known as SNPs) to
  20     characterize our collection. Polymorphic markers that we
  21     develop will also be useful to our stakeholders (e.g. tomato
  22     breeders) for saturating genetic maps and marker-assisted
  23     selection.</p>
  24
  25     <p>Tomato is ideal for pioneering SNP prediction and confirmation because of the
  26     wealth of publicly available DNA sequence data. Baldo has
  27     designed and implemented a high-throughput Expressed Sequence
  28     Tag (EST) analysis system which takes a NCBI Unigene set as
  29     input, and produces high-quality annotation and consensus
  30     sequences of subclusters, virtual mapping of consensus
  31     sequences by matching to known markers, SNP predictions, and
  32     SSR discovery. An additional module designs and selects optimal
  33     PCR primers flanking the regions of interest. Using the more
  34     than 150,000 EST and cDNA sequences from over 15 cultivars
  35     comprising the 3,000+ member Unigene set for <em>L.
  36     esculentum</em> in Genbank, 2,527 SNPs in 764 Unigenes were predicted. In 2004 we tested 85
  37     independent amplicons from the 764 Unigenes for predicted SNPs
  38     by sequencing two or three cultivars per amplicon. We
  39     discovered 62 SNPs and 13 small insertion/deletion
  40     polymorphisms in 21 amplicons. For the 64 remaining amplicons,
  41     one primer pair did not amplify, thirty two showed no evidence
  42     of the predicted SNP, 20 appeared heterozygous or gave multiple
  43     PCR bands, and 11 gave insufficient data (poor quality
  44     sequence, fragment too large to sequence predicted SNP site, or
  45     data from only one cultivar). Based on the 53 amplicons that
  46     gave clear results thus far, this method discovered cultivated
  47     tomato SNPs with approximately 21-fold more efficiency compared
  48     to sequencing random genomic DNA (1 SNP per 300 nucleotides
  49     versus 1 SNP per 7 kb). We have submitted a manuscript for
  50     publication of the 21 polymorphic markers and are continuing development
  51     and testing of the remaining set of 64 of the 85 originally
  52     tested.</p>
  53
  54     <p>We propose to
  55     develop and test the remaining 679 Unigenes with predicted SNPs
  56     in a collaborative effort with private companies such as
  57     Campbell's, Western Seed, Syngenta/Roger's Seed,
  58     Rijk Zwaan, Zeraim Gedera, and other interested parties. Based
  59     on our results we anticipate successfully developing at least
  60     25\% of the 764 Unigenes (191 loci) into polymorphic markers by
  61     sequencing two to three tomato cultivars with predicted SNPs
  62     among them. This will entail - obtaining the minimal set of
  63     cultivars needed based on NCBI's original EST data,
  64     growing the cultivars in PGRU's greenhouse and isolating
  65     DNA from leaf tissue, PCR primer design and PCR amplification
  66     for the remaining 679 Unigenes for two or three cultivars each,
  67     DNA sequencing, and analyses of the sequence data. The
  68     anticipated cost of carrying out this project in-house at PGRU
  69     is detailed in the attached budget pages. Products will be
  70     robust PCR and sequencing primers for genomic DNA sequences,
  71     identification of polymorphic sites among the assayed cultivars
  72     for those sequences, and annotation of sequences including
  73     predicted proteins and matches to known tomato markers. All
  74     results will be published in peer-reviewed journals and all
  75     collaborators will have access to preliminary and pre-published
  76     data.</p>
  77
  78     <p>The proposed
  79     research is part of PGRU's "Conservation of
  80     Vegetable Crops" CRIS, Objective 2 Enhance the
  81     effectiveness of germplasm maintenance through the application
  82     of genomic sequencing and molecular marker techniques.
  83     It will serve as a model for discovery of enhanced value within crop
  84     germplasm when faced by limited molecular genetic diversity,
  85     ensuring the future viability of U.S. farms and a nutritious
  86     food supply.</p>
  87 <br />
  88     <h3>Budget</h3>
  89
  90     <table summary="" border="0" cellspacing="0" cellpadding="0" width="40\%">
  91       <tr>
  92         <td width="220"><strong><u>Item</u></strong></td>
  93         <td width="75"><strong><u>Year 1</u></strong></td>
  94         <td width="75"><strong><u>Year 2</u></strong></td>
  95         <td width="75"><strong><u>Total</u></strong></td>
  96       </tr>
  97 <tr><td><p>&nbsp;</p></td></tr>
  98       <tr>
  99         <td><strong>Materials</strong></td>
 100         <td></td>
 101         <td></td>
 102         <td></td>
 103       </tr>
 104 <tr><td><p>&nbsp;</p></td></tr>
 105       <tr>
 106         <td>PCR and DNA sequencing<br /> (\$4.95 per sample)</td>
 107         <td>\$12,997</td>
 108         <td>\$12,997</td>
 109         <td>\$25,994</td>
 110       </tr>
 111 <tr><td><p>&nbsp;</p></td></tr>
 112       <tr>
 113         <td>Primers</td>
 114         <td>\$11,270</td>
 115         <td>\$1,691</td>
 116         <td>\$12,961</td>
 117       </tr>
 118 <tr><td><p>&nbsp;</p></td></tr>
 119       <tr>
 120         <td>Instrument maintenance</td>
 121         <td>\$2,192</td>
 122         <td>\$2,192</td>
 123         <td>\$4,383</td>
 124       </tr>
 125 <tr><td><p>&nbsp;</p></td></tr>
 126       <tr>
 127         <td><strong>Labor</strong></td>
 128         <td></td>
 129         <td></td>
 130         <td></td>
 131       </tr>
 132 <tr><td><p>&nbsp;</p></td></tr>
 133       <tr>
 134         <td>Technician (GS-4)</td>
 135         <td></td>
 136         <td></td>
 137         <td></td>
 138       </tr>
 139 <tr><td><p>&nbsp;</p></td></tr>
 140       <tr>
 141         <td>&nbsp;&nbsp;&nbsp;&nbsp;salary</td>
 142         <td>\$24,698</td>
 143         <td>\$26,288</td>
 144         <td>\$50,986</td>
 145       </tr>
 146 <tr><td><p>&nbsp;</p></td></tr>
 147       <tr>
 148         <td>&nbsp;&nbsp;&nbsp;&nbsp;benefits</td>
 149         <td>\$7,409</td>
 150         <td>\$7,886</td>
 151         <td>\$15,296</td>
 152       </tr>
 153 <tr><td><p>&nbsp;</p></td></tr>
 154       <tr>
 155         <td>3 Supervisory scientists<br /> (5\% each)</td>
 156         <td>\$16,778</td>
 157         <td>>\$17,615</td>
 158         <td>\$34,393</td>
 159       </tr>
 160 <tr><td><p>&nbsp;</p></td></tr>
 161       <tr>
 162         <td><strong>Total materials and labor</strong></td>
 163         <td>\$75,344</td>
 164         <td>\$68,669</td>
 165         <td>\$144,013</td>
 166       </tr>
 167 <tr><td><p>&nbsp;</p></td></tr>
 168       <tr>
 169         <td><strong>Other Direct Costs</strong></td>
 170         <td></td>
 171         <td></td>
 172         <td></td>
 173       </tr>
 174 <tr><td><p>&nbsp;</p></td></tr>
 175       <tr>
 176         <td>PGRU overhead IRC (0.1905)</td>
 177         <td>\$14,353</td>
 178         <td>\$13,081</td>
 179         <td>\$27,434</td>
 180       </tr>
 181 <tr><td><p>&nbsp;</p></td></tr>
 182       <tr>
 183         <td><strong>Total Direct Costs</strong></td>
 184         <td>\$89,697</td>
 185         <td>\$81,750</td>
 186         <td>\$171,447</td>
 187       </tr>
 188 <tr><td><p>&nbsp;</p></td></tr>
 189       <tr>
 190         <td><strong>Indirect Costs</strong></td>
 191         <td></td>
 192         <td></td>
 193         <td></td>
 194       </tr>
 195 <tr><td><p>&nbsp;</p></td></tr>
 196       <tr>
 197         <td>ARS overhead (0.1111)</td>
 198         <td>\$9,965</td>
 199         <td>\$9,082</td>
 200         <td>\$19,048</td>
 201       </tr>
 202 <tr><td><p>&nbsp;</p></td></tr>
 203       <tr>
 204         <td><strong>Total Direct and<br /> Indirect Costs</strong></td>
 205         <td><strong>\$99,662</strong></td>
 206         <td><strong>\$90,832</strong></td>
 207         <td><strong>\$190,495</strong></td>
 208       </tr>
 209     </table>
 210
 211 <br /><br /><br /><br />
 212
 213 <h4>Breakdown of Sequencing Costs</h4>
 214
 215 <table summary="" border="0" cellspacing="0" cellpadding="0" width="50\%">
 216     <tr>
 217     <td width="89\%">number of genes</td>
 218     <td align="right">700</td>
 219     </tr>
 220 <tr><td><p>&nbsp;</p></td></tr>
 221     <tr>
 222     <td>number of cultivars</td>
 223     <td align="right">3</td>
 224     </tr>
 225 <tr><td><p>&nbsp;</p></td></tr>
 226     <tr>
 227     <td>sequencing reactions (forward and reverse)</td>
 228     <td align="right">2</td>
 229     </tr>
 230 <tr><td><p>&nbsp;</p></td></tr>
 231     <tr>
 232     <td>cost per sequence</td>
 233     <td>\$4.95</td>
 234     </tr>
 235 <tr><td><p>&nbsp;</p></td></tr>
 236     <tr>
 237     <td>cost</td>
 238     <td>\$20,795</td>
 239     </tr>
 240 <tr><td><p>&nbsp;</p></td></tr>
 241     <tr>
 242     <td>number of additional reactions (25\%) for redos</td>
 243     <td align="right">1050</td>
 244     </tr>
 245 <tr><td><p>&nbsp;</p></td></tr>
 246     <tr>
 247     <td>cost for redos</td>
 248     <td>\$5,199</td>
 249     </tr>
 250 <tr><td><p>&nbsp;</p></td></tr>
 251     <tr>
 252     <td>total sequencing cost</td>
 253     <td>\$25,994</td>
 254     </tr>
 255 <tr><td><p>&nbsp;</p></td></tr>
 256     <tr>
 257     <td>total number of sequencing reactions</td>
 258     <td align="right">5250</td>
 259     </tr>
 260 </table>
 261
 262 <br /><br />
 263
 264 <h4>Breakdown of Primer Costs</h4>
 265
 266 <table summary="" border="0" cellspacing="0" cellpadding="0" width="50\%">
 267     <tr>
 268     <td width="89\%">number of primer pairs</td>
 269     <td align="right">700</td>
 270     </tr>
 271 <tr><td><p>&nbsp;</p></td></tr>
 272     <tr>
 273     <td>forward and reverse</td>
 274     <td align="right">2</td>
 275     </tr>
 276 <tr><td><p>&nbsp;</p></td></tr>
 277     <tr>
 278     <td>size of primer</td>
 279     <td align="right">23</td>
 280     </tr>
 281 <tr><td><p>&nbsp;</p></td></tr>
 282     <tr>
 283     <td>cost per base</td>
 284     <td>\$0.35</td>
 285     </tr>
 286 <tr><td><p>&nbsp;</p></td></tr>
 287     <tr>
 288     <td>cost</td>
 289     <td>\$11,270</td>
 290     </tr>
 291 <tr><td><p>&nbsp;</p></td></tr>
 292     <tr>
 293     <td>number of additional primers (15\%) added for redesigns</td>
 294     <td align="right">210</td>
 295     </tr>
 296 <tr><td><p>&nbsp;</p></td></tr>
 297     <tr>
 298     <td>cost of redesigned primers</td>
 299     <td>\$1,691</td>
 300     </tr>
 301 <tr><td><p>&nbsp;</p></td></tr>
 302     <tr>
 303     <td>total primer cost</td>
 304     <td>\$12,961</td>
 305     </tr>
 306 <tr><td><p>&nbsp;</p></td></tr>
 307     <tr>
 308     <td>total number of primers</td>
 309     <td align="right">1610</td>
 310     </tr>
 311     </table>
 312
 313 <br /><br />
 314
 315 <h4>Estimated costs of PCR and sequencing per sample</h4>
 316
 317 <table summary="" border="0" cellspacing="0" cellpadding="0" width="70\%">
 318 <tr>
 319 <td width="25\%"></td>
 320 <td width="10\%"></td>
 321 <td width="10\%"><strong>cost per unit</strong></td>
 322 <td width="10\%"><strong>number used<br />per sample</strong></td>
 323 <td width="10\%"><strong>cost per sample</strong></td>
 324 </tr>
 325 <tr><td><p>&nbsp;</p></td></tr>
 326 <tr>
 327 <td>10ul unplugged pipette tips</td>
 328 <td></td>
 329 <td>0.0173</td>
 330 <td>1</td>
 331 <td>0.02</td>
 332 </tr>
 333 <tr><td><p>&nbsp;</p></td></tr>
 334 <tr>
 335 <td>200ul unplugged pipette tips</td>
 336 <td></td>
 337 <td>0.014</td>
 338 <td>2</td>
 339 <td>0.03</td>
 340 </tr>
 341 <tr><td><p>&nbsp;</p></td></tr>
 342 <tr>
 343 <td>10ul plugged pipette tips</td>
 344 <td></td>
 345 <td>0.049</td>
 346 <td>7</td>
 347 <td>0.34</td>
 348 </tr>
 349 <tr><td><p>&nbsp;</p></td></tr>
 350 <tr>
 351 <td>200ul plugged pipette tips</td>
 352 <td></td>
 353 <td>0.063</td>
 354 <td>2</td>
 355 <td>0.13</td>
 356 </tr>
 357 <tr><td><p>&nbsp;</p></td></tr>
 358 <tr>
 359 <td>large orifice 200ul unplugged pipette tips</td>
 360 <td></td>
 361 <td>0.026</td>
 362 <td>2</td>
 363 <td>0.05</td>
 364 </tr>
 365 <tr><td><p>&nbsp;</p></td></tr>
 366 <tr>
 367 <td>large orifice 200ul plugged pipette tips</td>
 368 <td></td>
 369 <td>0.058</td>
 370 <td>2</td>
 371 <td>0.12</td>
 372 </tr>
 373 <tr><td><p>&nbsp;</p></td></tr>
 374 <tr>
 375 <td>50ul plugged pipette tips</td>
 376 <td></td>
 377 <td>0.05</td>
 378 <td>2</td>
 379 <td>0.10</td>
 380 </tr>
 381 <tr><td><p>&nbsp;</p></td></tr>
 382 <tr>
 383 <td>black 96-well clini plates</td>
 384 <td></td>
 385 <td>0.02</td>
 386 <td>2</td>
 387 <td>0.04
 388 </td>
 389 </tr>
 390 <tr><td><p>&nbsp;</p></td></tr>
 391 <tr>
 392 <td>PCR plates</td>
 393 <td></td>
 394 <td>0.07</td>
 395 <td>2</td>
 396 <td>0.14</td>
 397 </tr>
 398 <tr><td><p>&nbsp;</p></td></tr>
 399
 400 <tr>
 401 <td>1.5ml tubes</td>
 402 <td></td>
 403 <td>0.03</td>
 404 <td>1</td>
 405 <td>0.03</td>
 406 </tr>
 407 <tr><td><p>&nbsp;</p></td></tr>
 408 <tr>
 409 <td>Molecular Probes picogreen reagent<br />(1 includes forward and reverse)</td>
 410 <td></td>
 411 <td>0.14</td>
 412 <td>0.5</td>
 413 <td>0.07</td>
 414 </tr>
 415 <tr><td><p>&nbsp;</p></td></tr>
 416 <tr>
 417 <td>dNTPs</td>
 418 <td></td>
 419 <td>0.05</td>
 420 <td>2.2</td>
 421 <td>0.11</td>
 422 </tr>
 423 <tr><td><p>&nbsp;</p></td></tr>
 424 <tr>
 425 <td>Promega GoTaq PCR enzyme</td>
 426 <td></td>
 427 <td>0.22</td>
 428 <td>2.2</td>
 429 <td>0.48</td>
 430 </tr>
 431 <tr><td><p>&nbsp;</p></td></tr>
 432 <tr>
 433 <td>EdgeBio PCR clean-up<br />(1 includes forward and reverse)
 434 </td>
 435 <td>
 436 </td>
 437 <td>1.03</td>
 438 <td>0.5</td>
 439 <td>0.52</td>
 440 </tr>
 441 <tr><td><p>&nbsp;</p></td></tr>
 442 <tr>
 443 <td>ABI BDT cycle sequencing enzyme</td>
 444 <td>
 445 </td>
 446 <td>1.57</td>
 447 <td>1</td>
 448 <td>1.57</td>
 449 </tr>
 450 <tr><td><p>&nbsp;</p></td></tr>
 451 <tr>
 452 <td>EdgeBio sequencing rxn. clean-up</td>
 453 <td></td>
 454 <td>0.52</td>
 455 <td>1</td>
 456 <td>0.52</td>
 457 </tr>
 458 <tr><td><p>&nbsp;</p></td></tr>
 459 <tr>
 460 <td>ABI sequencing polymer POP6</td>
 461 <td></td>
 462 <td>0.26</td>
 463 <td>1</td>
 464 <td>0.26</td>
 465 </tr>
 466 <tr><td><p>&nbsp;</p></td></tr>
 467 <tr>
 468 <td>ABI 3100 capillary array</td>
 469 <td></td>
 470 <td>0.43</td>
 471 <td>1</td>
 472 <td>0.20</td>
 473 </tr>
 474 <tr><td><p>&nbsp;</p></td></tr>
 475 <tr>
 476 <td></td>
 477 <td></td>
 478 <td></td>
 479 <td align="right"><strong>total:</strong></td>
 480 <td><strong>\$4.95</strong></td>
 481 </tr>
 482 </table>
 483
 484 <br /><br />
 485
 486 <h4>ABI 3100 DNA sequencer maintenance</h4>
 487
 488 <table summary="" border="0" cellspacing="0" cellpadding="0" width="50\%">
 489 <tr>
 490 <td width="16\%">lower polymer block</td>
 491 <td width="1\%"></td>
 492 <td width="1\%">\$2,200</td>
 493 </tr>
 494 <tr><td><p>&nbsp;</p></td></tr>
 495 <tr>
 496 <td>reserve polymer syringe</td>
 497 <td></td>
 498 <td>\$258</td>
 499 </tr>
 500 <tr><td><p>&nbsp;</p></td></tr>
 501 <tr>
 502 <td>array-fill syringe</td>
 503 <td></td>
 504 <td>\$150</td>
 505 </tr>
 506 <tr><td><p>&nbsp;</p></td></tr>
 507 <tr>
 508 <td>maintenance contract (10\% over 2 years)</td>
 509 <td></td>
 510 <td>\$1,775</td>
 511 </tr>
 512 <tr><td><p>&nbsp;</p></td></tr>
 513 <tr>
 514 <td></td>
 515 <td align="right"><strong>total: </strong></td>
 516 <td><strong>\$4,383</strong></td>
 517 </tr>
 518 </table>
 519
 520 <br /><br /><br /><br />
 521
 522 <h3>Budget narrative</h3>
 523
 524 <h4>Primers</h4>
 525
 526     <p>Custom-synthesized oligos are purchased from
 527     Integrated DNA Technologies, Inc. PCR/sequencing oligos cost
 528     \$0.35/base at 25 nmole scale. Generally 4 pmol primer is used
 529     per PCR or sequencing reaction. We estimate 1,610 primers will
 530     be sufficient to PCR and sequence 700 loci taking into account
 531     needs for occasionally redesigning primers and replenishing
 532     primer stocks (15\% added). &nbsp; 23-mer x \$0.35 x 1,610 =
 533     \$12,961</p>
 534
 535 <h4>Laboratory costs</h4>
 536
 537     <p>We routinely test all newly synthesized PCR primers across the 2
 538     or 3 genomic DNAs to be sequenced in small volume PCR
 539     reactions. After this initial optimization a larger volume (50
 540     ul) PCR reaction is performed, PCR products are cleaned using
 541     an EdgeBioSystems Quickstep kit, DNA is quantified in a
 542     picogreen assay, ABI BDT ver. 3.1 cycle sequencing reactions
 543     are performed, samples are cleaned on an EdgeBioSystems DTR
 544     plate, dried down, resuspended in formamide, and run on the ABI
 545     3100 capillary sequencer.</p>
 546
 547     <p>Itemized costs per sample are in the budget
 548     table. Plastic disposables include pipette tips, 96-well
 549     plates, and eppendorf tubes. Disposable capillary arrays for
 550     the ABI 3100 cost \$695 each and last approximately 100 runs (1
 551     run = 16 samples). Costs of reagents including dNTPs, GoTaq and
 552     BDT enzymes, picogreen, POP6 polymer, and EdgeBio kits are
 553     estimated on a per sample basis. Cost per sequence = \$4.9513 x
 554     5,250 sequences = \$25,994</p>
 555
 556 <h4>Instrument maintenance</h4>
 557
 558     <p>The throughput of our ABI 3100 DNA sequencer is two 96-well plates
 559     in 30 hours. For 5,250 reactions this is equivalent to 8 months
 560     of operation \@ 4 hours per day. We replace the lower polymer
 561     block, array-fill syringe, and reserve polymer syringe
 562     approximately every 6 months as routine maintenance. In 2004
 563     the ABI service maintenance contract cost \$8,750. We request
 564     \$2,192 per year to defray instrument maintenance
 565     costs.</p>
 566
 567 <h4>Labor</h4>
 568
 569     <p>One full-time ARS Biological Science Technician (GS-4) is requested
 570     to carry out the majority of the labor for this project. Salary
 571     was estimated at entry level with 30\% added for benefits. There
 572     will be three supervisory scientists whose costs are estimated
 573     at 5\% of their salary and benefits each. Their respective roles
 574     can be described as follows - Vegetable Crops Curator Dr. Larry
 575     Robertson will be responsible for obtaining seed of required
 576     tomato cultivars, overseeing its planting and harvesting for
 577     tissue collection, and subsequent sample tracking and data
 578     curation. Larry has developed a database for PGRU for efficient
 579     tracking of samples from planting, through all laboratory
 580     assays, to final storage of molecular data. Bioinformaticist
 581     Dr. Angela Baldo will be responsible for all
 582     computational marker discovery: identification and downloading
 583     of public EST, cDNA, and genomic sequences, high-throughput
 584     in-house clustering, annotation, <em>in silico</em> mining for markers, and high-throughput
 585     primer design. Molecular Biologist Dr. Joanne Labate's
 586     primary responsibility on this project will be to train the
 587     technician in laboratory techniques and to oversee the
 588     collection and analyses of the molecular data, ensure quality
 589     control of laboratory-generated data, and dissemination of high
 590     quality data to collaborators.</p>
 591
 592 <h4>Overhead</h4>
 593
 594     <p>Local overhead at PGRU is estimated as 16\% of total direct costs.
 595     National overhead for ARS is estimated as 10\% of total direct
 596     and indirect costs.</p>
 597
 598 <h4>Facilities and equipment</h4>
 599
 600     <p>Physical facilities include three greenhouses with a total of 7500
 601     ft<sup>2</sup> for growing plants. The 1400 ft<sup>2</sup>
 602     laboratory is well-equipped to efficiently generate DNA
 603     sequence data. Major equipment includes an MJ Research Tetrad2 and two BioRad
 604     iCycler thermocyclers, one ABI 3100 and one ABI 310 Genetic
 605     Analyzer, a Tecan Genesis RSP 150 robotic liquid handling
 606     system, a plant tissue grinder (GenoGrinder), a
 607     refrigerated-centrifuge and a speed-vac that can hold 96-well
 608     plates, an Alpha Innotech FluorChem 8900 imaging and analysis
 609     system, and a 96-well plate reader for fluorescence and
 610     absorbance assays. We also have all necessary small equipment that we require such
 611     as microcentrifuges, incubators, shakers, autoclave, agarose
 612     gel rigs and power supplies, electronic multi-channel pipettes,
 613     -20&deg;C and -80&deg;C freezers, a freeze-drier,
 614     microcomputers, etc.</p>
 615
 616     <p>We have at our
 617     disposal a Dell PowerEdge 6600 server with four 2.4GHz Intel
 618     side-bus processors, 16GB of RAM, and 876GB of storage in a
 619     RAID configuration, with an additional hot spare. This server
 620     currently runs Linux kernel 2.4, and shoulders the majority of
 621     the Unit's computational analyses. We have two secondary servers:
 622     a Dell 530 Workstation with a i686 single 1.7GHz processor
 623     server with 512MB memory, and 80GB of storage; Dell PowerEdge 4100 with
 624     200MHz processor with 256MB of memory and 22GB of storage, and
 625     a desktop workstation, all running Linux. Finally we have a
 626     Sony PCG-GRX700P notebook with i686 architecture, 2.20GHz,
 627     512MB RAM, and a 60GB hard drive, running a notebook-optimized
 628     version of the same Linux distribution. All five Linux machines are
 629     configured such that they can read and write to the shared
 630     Novell fileserver (Dell PowerEdge 2650, single processor
 631     1.8GHz, 1MB RAM, with 76GB of storage) and each other's hard
 632     drives. The rest
 633     of the computer network available for this project consists of
 634     approximately 14 Dell desktop PCs running Microsoft Windows
 635     connected by the Novell print and fileserver mentioned
 636     above.</p>
 637
 638 END_HEREDOC
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