Genetics October 2004

genetics@lists.oulu.fi

4 participants
6 discussions

ABI3730-info
by Helmi Kuittinen 24 Nov '04

24 Nov '04

Hello DNA analyzers, Great that so many attended the 3730 meeting on Tuesday. Those that did not participate in the practical demonstrations, please do not hesitate to ask Johanna Leppälä, Laura Kvist, Sami Sivula or Marjut Kreivi to help you in starting to work with the new machine. You can always also contact Jussi Vanhatalo from Applied Biosystems (09-69379427). There are printed guides for the software available in room PT331. Tutorials for GeneMapper and SeqScape and a guide for sequencing chemistry are available only as CDs. I have downloaded these CDs on the server BIOL4 and you can copy them onto your PC. The two training CDs are quite big and you can also run them directly on CD (CDs are in PT331). When you have samples run in the 3730, the idea is that the machine is told to send your data to the server (BIOL4) into your personal folder. You can then transfer or copy the data from the server to your own computer, where you analyze it with the appropriate software. You will also be able put the sample information in a file to a shared folder (shared/future_runs/36cm_aray or /50cm_array) in the server. Hannele will use that file for the run and then she will move it to the "processed runs" folder. There will be template excell files and instructions available under the "Shared" folder for making these sample informations files. In this way the one PC in PT331 can only be used for running the machine. I have also put guides and training programs (3730 DNA Analyzeres User Guide, 3730 Sequencing chemistry guide, GeneMapper 3.5 training Seqscape 1.1.1 training) under a folder called "Shared/guides/". To get an access to the server BIOL4, you need to write an e-mail to Kai Niemelä, and tell him your name, domain name and whether you are a student or a researcher (graduate students are reseachers). If you want to keep a copy of your data in that server it is possible for some time, we will just need to follow how fast the hard disc will get filled. The software that is used for analyzing the data (SeqA, GeneMapper, and Seqscape) can be donwloaded to your own PC. Seqscape and GeneMapper work only in quite efficient PCs, so pay attention to the requirements. Seqscape and SeqA work with Windows 2000 and XP. The current version of Genemapper only works with Windows 2000, the new (will be available in December) works with XP too. There are three registration codes for the programs and thee simultaneous users are allowed. If you want to download a program, please contact me or Johanna Leppälä. I have attached the special offer for the first order ("kertatilaus laitehankinnan yhteydessä") that I got from Applied Biosystems. I will receive prices for the reagent agreement for new consumables later, maybe not before next Tuesday. I will forward them as soon as I get them. The preliminary information was that in the reagent agreement we will have 35% reduction for plasticware and at least 10% for other things (buffer, polymer, size standards, capillaries); for oligos there was no info. The existing reagent agreement is of course valid and it already includes e.g. the Big Dye kits. The reference price lists of Genomic assays and custom oligos, and Genetic analysis reagents and application kits are available in PT331 and if needed I can send them electronically. I suggest that you compare the regular agreement and the special offer prices, and of course prices from other suppliers, and let me know if you want to order something with the special offer prices. We hope that we will be able to send the order soon, lets aim for Thursday next week. We make a joint order and Sisko will divide the bill for each group accordingly. There are some consumable that need not to be ordered from Applied, e.g. plates (check!). Of the dye set G5, PET, NED, VIC and the size standard LIZ are only produced by them, and with a licence by some other company. At least TAG Copenhagen has a cheaper dye that can be used instead of VIC. We think that it is best that every user/group buys their formamide, because for sequencing there is also the option to put the samples in water, and the sample volume is now much higher (10-20ul). The costs of polymer, buffer, septas etc. will be shared as before, based on the number of samples run by each group. Last, I have booked a computer class (TH118) for the next training session, for 27.-29.9. 8-16. There will be more information in September. I hope these days suit many of you. With regards, Helmi Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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PT304 printteri kytketty irti
by Liisa Raisanen 27 Oct '04

27 Oct '04

Hei, ilmeisen viruksen takia PT304 printteri suoltaa taukoamatta muutamaa hassua merkkiä vaille tyhjää paperia. Otin töpselin irti kunnnes asiaan saadaan korjaus. Liisa Räisänen University of Oulu Department of Biology/Genetics PO.Box 3000 FIN-90014 Oulu Finland Liisa.Raisanen(a)oulu.fi fax 358 8 553 1061 tel 358 8 553 1792

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gene mapping
by Pekka Pamilo 13 Oct '04

13 Oct '04

Hi The web site of the Graduate Schoolof Population Genetics at http://cc.oulu.fi/~biolwww/PopGenSchool/uutisia.html has now information about the gene mapping course at Hailuoto, November 17-19. The web site has the schedule and information on registration. If you have already pre-registered, you don't have to do that again (unless there are any changes). The course is in English even though the web site is in Finnish. Pekka

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(no subject)
by Hannele Parkkinen 12 Oct '04

12 Oct '04

Hei! VWR international tulee esittelemään uutuuksiaan huomenna Keskiviikkona klo 12.30 perimän kahvihuoneeseen.Pullatarjoilusta ei ole tietoa,mutta toivotaan siitä huolimatta osanottoa. t.Hannele

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Biolaskennan peruskurssi 25.-26.11.2004 (fwd)
by Minna Ruokonen 06 Oct '04

06 Oct '04

---------- Forwarded message ---------- Date: Mon, 4 Oct 2004 14:13:48 +0300 (EEST) From: Kimmo Mattila <kkmattil(a)csc.fi> To: bioclients(a)csc.fi Cc: bioscience(a)csc.fi Subject: Biolaskennan peruskurssi 25.-26.11.2004 Hei, CSC järjestää biolaskennan peruskurssin 25. - 26.11. 2004. Kurssilla käsitellään tietokantahakuja, sekvenssianalyysiä ja fylogenetiikkaa mm. EMBOSS-, SRS-, Clustal- ja Phylip-ohjelmistoja käyttäen. Lisäksi tutustutaan Blast- ja Smith-Waterman -hakuihin Gepardi-erikoispalvelimellamme. Tarkempaa tietoa kurssista ja ilmoittautumisesta löytyy sivulta: http://www.csc.fi/molbio/opetus/bioperus2004.html Tiedot muista tulevista bioinformatiikkakursseista löytyvät sivulta: http://www.csc.fi/molbio/opetus/index.html Terv. Kimmo Mattila --------------------------------------------------------------------- CSC organises a course: Basics in Bioinformatics 25. - 26.11. 2004 The course covers basics of database searches, sequence analysis and phylogenetics using EMBOSS, SRS, Clustal and Phylip-packages. It also includes Blast-searches using our specialized Gepardi-server. Please note that the course is in Finnish. More information on the course and registration can be found at: http://www.csc.fi/molbio/opetus/bioperus2004.html Other bioinformatics courses organized at CSC are announced at http://www.csc.fi/molbio/opetus/index.html. Regards, Kimmo Mattila

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gene mapping
by Pekka Pamilo 01 Oct '04

01 Oct '04

The Graduate School of Population Genetics will have a course on gene mapping at the Perämeri Research Station in Hailuoto in November 17-19 (Wednesday to Friday). The course will start Wednesday morning in such a way that it is possible to arrive from Oulu in the morning. The graduate school covers the travel and accomodation expenses. The detailed schedule will be given later, and the teachers are: Vesa Ollikainen (Centre for Scientific Computing, CSC) will lecture on gene mapping with practical examples using the programs of CSC, on Wednesday and Thursday. A computer class will be moved from Oulu to Hailutoto for the course. Mikko Sillanpää (Dept of Mathematics and Statistics of Helsinki University) will lecture on association mapping David Remington (University of Greensboro) will lecture on QTL mapping Inform me if you plan to attend. We try to get the detailed schedule soon. Pekka

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Genetics October 2004