histoni

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Protein Production and Analysis
by Lloyd Ruddock 10 Oct '08

10 Oct '08

Dear all, If you are on the Protein Production and Analysis course and have read the manual you will have noticed one "cut and paste" too many. On page 2 it says the practicals begin at 8.00 on Thursday 1st february. They of course start on Monday 13th October - but still at 8.00 sharp. The demonstrators will start with an introduction to the practical class and if you are late you will miss this important information, so please no repeat of todays "starting sharp" problems. I hope you have a good weekend. Best wishes, Lloyd

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muutoksia lukujärjestykseen 9.10.08/ changes in timetable
by Jari Heikkinen 09 Oct '08

09 Oct '08

Hei This information do not concern Int MSc students ! Seuraavien kurssien kohdalle on tullut muutoksia / Timetables of following courses have been changed Protein chemistry II katso muutokset/ see changes: http://www.biochem.oulu.fi/studies/opetusohjelma/paivitetytmuutokset_syksy0… http://www.biochem.oulu.fi/studies/opetusohjelma/Opetusohjelma_syksy_2008.p… Kurssin Practical teaching for biochemists lopullinen aikataulu löytyy opetuksen ajakohtaisista ilmoituksista: http://www.biochem.oulu.fi/studies/opetusohjelma/PRACT_TEACH.pdf Lloydin ilmoittamaan alustavaan aikatauluun on tullut 2 muutosta: ma 24.11 ja ke 3.12 luentoja on siiretty tunnilla päällekkäisen opetuksen välttämiseksi. terv, jari Jari Heikkinen E-Mail jari.heikkinen(a)oulu.fi Department of biochemistry Office phone +358-8-5531208 University of Oulu FAX +358-8-5531141 P.O.B 3000 Home phone +358-8-5546519 FIN-90014 UNIVERSITY OF OULU Mobile phone 0400-380535 Oulu, Finland

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Fuksiaiset tänään klo 20-> @Teekkaritalo / Party tonight
by Susanna Teppo 09 Oct '08

09 Oct '08

Älkääpä unohtako tämän iltaisia fuksiaisia. Just to remind you of the party tonight at Teekkaritalo. _________________ Mitä tapahtuu? - Histonin eli teidän kaikkien syksyinen kohokohta Fuksiaiset Koska? - ensi torstaina klo 20->. Missä? - Teekkaritalolla Mitä kantsii tietää? - sauna kuumana, oma pyyhe mukaan - omien makkaroiden paistomahdollisuus - histoni tarjoaa pientä purtavaa - klo 22.00 alkaen edullinen arpamyynti, jossa palkintona kalja/siideri/lonkero - omat juomat ovat ehdottomasti sallittuja - sisäänpääsy 1 euro, fuksit ilmaiseksi - dresscode haalarit Suuresti tervetuloa uudet ja vanhat. __________________ What? - Histoni´s party for freshmen (first year students) and all biochemistry students When? - Next Thursday starting at 20.00 -> Where? - Teekkaritalo, address Kalervontie 7 What´s in there? - music, chatting.. ordinary student party - sauna is on, bring a towel if you wish to go - possibility to fry one´s own sausages - histoni offers snacks - from 22.00 there is a possibility to buy a lot with a beer/cider/long drink as a price - own beverages are allowed - cover charge 1 euro (- dresscode: student overalls if one has ones) You are very welcome.

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Fwd: [Histoni-hallitus] HAE AASIAN OHJELMAAN 2009, haku päättyy 18.11.2008! Apply for the Asian Programme!
by Elina Mirjami Jokinen 08 Oct '08

08 Oct '08

----- Forwarded message from sianle(a)utu.fi ----- Date: Wed, 08 Oct 2008 10:10:06 +0300 From: Silja Keva <sianle(a)utu.fi> Reply-To: Silja Keva <sianle(a)utu.fi> Subject: [Histoni-hallitus] HAE AASIAN OHJELMAAN 2009, haku päättyy 18.11.2008! Apply for the Asian Programme! To: Silja Keva <sianle(a)utu.fi> Välitettäväksi jäsenistöllenne, kiitos! --------------------------------------- For info in English, please see below! SUUNNITTELETKO URAA AASIASSA? OLETKO KIINNOSTUNUT ESIM. KIINASTA, JAPANISTA, THAIMAASTA TAI INTIASTA? Jos haluat oppia Itä- ja Kaakkois-Aasian kulttuurihistoriasta, yhteiskunnista ja liiketoiminnasta, osallistu Aasian ohjelmaan 2009. Valtakunnallinen Aasian ohjelma (25 - 31 op) on monitieteinen perusopintojen tasoinen opintokokonaisuus. Ohjelma antaa vankan tiedollisen pohjan Itä- ja Kaakkois-Aasiasta opiskelijoille, joiden opinto- ja urasuunnitelmat liittyvät Aasiaan. Opintokokonaisuuden järjestää valtakunnallinen Itä- ja Kaakkois-Aasian yliopistoverkosto ja siihen voivat hakea kaikki suomalaisissa yliopistoissa ja ammattikorkeakouluissa opiskelevat opiskelijat. Opetus järjestetään verkko-opetuksena Moodle-oppimisympäristössä (sis. verkkoluentoja, -kursseja ja - harjoituksia). Ohjelmassa tarjotaan viisi vapaavalinnaista kurssia. Ohjelmasta voi koota sivuaineeksi soveltuvan opintokokonaisuuden tai siitä voi suorittaa yksittäisiä kurssiosioita. Sivuainekokonaisuutta varten on suoritettava neljä (4) kokonaista kurssia ja vähintään 25 opintopistettä. Kurssi A on suomeksi ja kurssit B, C, D ja E ovat englanniksi. Ohjelmassa voi suorittaa seuraavia kursseja: A. Itä- ja Kaakkois-Aasian kulttuurihistoria, kevät 2009 (valittavana 6 tai 3 op) B: Society and Politics in East and Southeast Asia, kevät 2009 (valittavana 6 tai 2 op ) C: Business in East and Southeast Asia, syksy 2009 (valittavana 7, 5 tai 2 op) D: Language and Communication in East and Southeast Asia, syksy 2009 (6 op) E: India in World Politics, syksy 2009 (6 op) Ohjelmaan voivat hakea kaikki opiskelijat, joilla on voimassaoleva opinto-oikeus jossakin suomalaisessa yliopistossa tai korkeakoulussa. Ohjelmaa ei suositella ensimmäisen vuoden opiskelijoille. Hakulomake ja lisätietoja: Itä- ja Kaakkois-Aasian yliopistoverkoston www-sivut: http://www.asianet.fi/asianet/opetus/ao_haku2009.html Itä- ja Kaakkois-Aasian yliopistoverkosto Suunnittelija Silja Keva, puh. 02-333 8897, s-posti: silja.keva(a)utu.fi ---------------------------------------------------------------------- ASIAN STUDIES PROGRAMME 2009 APPLICATION DEADLINE 18.11.2008 The Asian Studies Programme (25 sp/ECTS) is an interdisciplinary study programme, which offers students basic knowledge of East and Southeast Asia. The programme also includes a course on India (?India in the World Politics?).The programme is organised by the Finnish University Network for East and Southeast Asian Studies. The programme consists of online courses with lectures, materials and exercises and it is organised in the Moodle learning environment on the Internet. The programme can be taken as a minor subject or in smaller course entities. In order to get a degree for a minor subject, the student must finish four complete courses and at least 25 credits. The languages of instruction are Finnish (course A) and English (courses B,C, D and E). In 2009 the following courses are offered: A: Cultural History of East and Southeast Asia, spring 2009 (in Finnish, options: 6 sp or 3 sp) B: Society and Politics in East and Southeast Asia, spring 2009 (in English, options: 6 sp or 2 sp) C: Business in East and Southeast Asia, autumn 2009 (in English, options: 7 sp, 5 sp, or 2 sp) D: Language and Communication in East and Southeast Asia, autumn 2009 (in English, options: 6 sp) E: India in World Politics, autumn 2009 (in English, options: 6 sp) The programme is open for all students in Finnish universities and polytechnics, who hold a valid study right. It is not recommended for first year students. Additional information and application form from: http://www.asianet.fi/asianet/english/teaching/ao_application2009.html Finnish University Network for East and Southeast Asian Studies Coodinator Juha Tähkämaa, tel. 02-333 5367, e-mail: juhtah(a)utu.fi Planning Officer Silja Keva, tel. 02-333 8897, e-mail: silja.keva(a)utu.fi -- Silja Keva Suunnittelija / Planning Officer Itä-ja Kaakkois-Aasian yliopistoverkosto / Finnish University Network for East and Southeast Asian Studies c/o Itä-Aasian tutkimus- ja koulutuskeskus/ Centre for East Asian Studies Arwidssoninkatu 1, rak. 10 20014 Turun yliopisto / University of Turku, Finland tel. +358 2 333 8897 http://www.asianet.fi -- Silja Keva Suunnittelija / Planning Officer Itä-ja Kaakkois-Aasian yliopistoverkosto / Finnish University Network for East and Southeast Asian Studies c/o Itä-Aasian tutkimus- ja koulutuskeskus/ Centre for East Asian Studies Arwidssoninkatu 1, rak. 10 20014 Turun yliopisto / University of Turku, Finland tel. +358 2 333 8897 http://www.asianet.fi _______________________________________________ Histoni-hallitus mailing list Histoni-hallitus(a)lists.oulu.fi http://lists.oulu.fi/mailman/listinfo/histoni-hallitus ----- End forwarded message -----

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No sports tomorrow Thursday
by Olli Niemitalo 08 Oct '08

08 Oct '08

Histoni does not organize sports tomorrow Thursday because the time coincides with the freshmen party/orienteering. You can still use our sport hall reservation if you wish. -olli

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Results of survey: Computing skills in biochemistry
by Olli Niemitalo 07 Oct '08

07 Oct '08

Last year a survey was circulated about biochemists' use of computers and automated methods of data analysis. A report of the results is now available: http://www.student.oulu.fi/~oniemita/Computing%20skills%20in%20biochemistry… I have copy-pasted the interesting bits below. -olli D I S C U S S I O N , C O N C L U S I O N S A N D R E C O M M E N D A T I O N S A satisfactory number of 119 people completed the survey, mainly students and PhD students. In general, people responded to the project in an encouraging manner. Much information was gained from the answers. COMPUTING SKILL LEVELS The essential computer-related skills for biochemists are the use of office software: word processing, presentation and spreadsheet software, and the use of literature databases. Spreadsheets are a problem area for some, and literature databases for some, but otherwise biochemists from Oulu have good skills in these. Many working biochemists also need to do image processing, statistics and data analyses. These areas are not covered well by teaching in Oulu. Also courses demand a higher level of skill than is available in spreadsheets, literature databases, data analysis and graphing and statistics. Basic spreadsheet, literature database and image processing skills can be taught quite easily, but to provide the students with the needed statistics and data analysis and graphing skills would require more added teaching. In general, biochemists from Oulu have sufficient word processing skills and quite good presentation software and literature database skills, but lack increasingly in more mathematically oriented subjects. HOW TO IMPROVE TEACHING Some methods of data analysis may be out-dated by more recent and more advanced methods. If a new method improves accuracy or usefulness of results, its use should be encouraged especially in teaching. A highly automated analysis method can be pedagogically useful if it allows the student to better focus on the big picture rather than on computational details of a method. It seems likely that biochemists from different levels would take part in courses about computer use tailored specifically for their needs, if such were implemented. Spreadsheets and image processing should be taught in an organized manner, because the basics can be taught very efficiently and would already be useful on many courses and would give a good basis for further learning. If teaching resources allow, students would also benefit greatly from improved teaching of statistics and data analysis, preferably using real biochemical problems as exercises. Also reference managing would be good to learn at an early time. Individual software solutions are not very long-lived, so teaching students the detailed use of single programs may not be very purposeful. Most biochemists and biochemistry students use Windows for work and/or studies. A minority uses Linux or Mac. When possible, the availability of compatible software to software used in teaching should be confirmed for these computer platforms. New students are very familiar with Internet, and for them it is a natural medium for communication. Most teachers accept work reports from students in electronic form while some teachers are more used to working with paper reports and prefer things that way. Internet is already nearly as popular a distribution media for course material as paper. However, putting on-line material that is copied without permission from Internet, from books or from articles or using such material in a PowerPoint presentation is in conflict with the Finnish copyright law. To allow photocopying of copyrighted works, the Ministry of Education pays yearly to Kopiosto, a copyright organization. The Finnish law is lagging in that such an agreement does not yet exist for electronic copies. The law is expected to improve eventually. Distance learning systems are rarely used by teachers and students' opinions on the usefulness of Optima were mixed. There is clearly interest in using distance learning systems more, but that would require establishing training sessions for teachers and students. Students would also benefit from an on-line FAQ (Frequently Asked Questions) concerning all subjects encountered in biochemistry studies. This would be easy to establish and students could produce much of the content. MODERN METHODS FOR BIOCHEMISTS There is a wide variety of computer programs available that can be useful in biochemistry. Based on the survey, some potentially interesting ones are listed in the following table. Biochemists are encouraged to experiment with these for their benefit. IMAGE ANALYSIS AND PROCESSING Adobe Photoshop, Market leader graphics editor Corel Draw, Vector graphics editor with bitmap editing capabilities Adobe Illustrator, Vector graphics editor GIMP, Graphics editor – free BioimageXD, Image analysis for microscopy – free ImageJ, Java-based graphics editor – free Imaris, Market leader in 3D and 4D image analysis for microscopy Inkscape, Vector graphics editor – free Bio-Rad Quantity One, Gel and blot analysis and colony counting Image-Pro, Scientific image analysis IrfanView, Image viewer and processor – free STATISTICS, DATA ANALYSIS AND GRAPHING SPSS, Statistics R, Statistics – free Matlab, Numerical computing environment Scilab, Numerical computing environment – free SigmaPlot, Data analysis and graphing OriginLab Origin, Data analysis and graphing – free with license from https://www.oulu.fi/jakelu GraphPad Prism, Data analysis and graphing WaveMetrics IGOR, Data analysis and graphing Excel, Spreadsheet OpenOffice.org Calc, Spreadsheet – free Gnuplot, Graphing – free GraFit, Data analyis and graphing Umetrics SIMCA-P+, Multivariate data analysis Umetrics MODDE, Design of experiments and optimization TableCurve, Curve fitting SEQUENCE ANALYSIS Biology workbench, On-line work environment for sequence analysis BioEdit, Sequence alignment editor GeneDoc, Sequence alignment editor Chromas, Chromatogram analysis Invitrogen NTI 10 and VectorNTI, Work environments for sequence analysis DNASTAR Lasergene, Sequence analysis toolset and environment MAFFT, Sequence alignment – free NEBcutter, Finds open reading frames and restriction sites – free Webcutter, Finds restriction sites – free REFERENCE MANAGING EndNote, Bibliography manager Reference Manager, Bibliography manager MOLECULAR VISUALIZATION Pymol, Molecular visualization – free Bodil, Molecular visualization and modeling -free ChemSketch, Chemical drawing tool ChemDraw, Chemical drawing tool Rasmol, Molecular visualization – free DeepView - Swiss-Pdbviewer, Molecular visualization and structural alignment – free Some laboratory equipment such as microscopes come with specialized software that can be useful also for doing other analyses. Also self-made programs can be useful for small tasks. Among biochemists, Visual Basic and Perl are the most popular programming languages that are not very hard to learn. It cannot be expected that all biochemists would do programming, but the skill may benefit those whose custom data processing and analysis needs are not met by existing programs. Some analysis environments also include their own programming languages that can be used. Very few biochemists currently use an electronic laboratory notebook, although such a system would improve quality, efficiency and collaboration. Electronic notebook entries are easy to search, index and link to. A laboratory-wide database of recipes and protocols could be established. The slow adoption of such systems is probably explained by that no-one likes to be the first to spend money in a commercial system that might not turn out to be as useful as expected. A complete electronic laboratory notebook solution can be obtained for about 700 USD per user (labtrack.com). Even a simple Word document can act as an electronic laboratory notebook. Such documents obtain the status of legal evidence through digital time-stamping, which may prove critical in patent disputes. Digital time-stamping proves that a document existed at the moment of time-stamping, and that its contents have remained unchanged since. A commercial, easy-to-use digital time-stamping service costs about 50 USD per user annually (surety.com). To protect from data loss, a properly implemented backup system must be in place when using electronic laboratory notebooks. Travel expenses and time could be saved by wider use of teleconferencing or video conferencing. For teleconferencing, software such as Skype, Google Talk, Windows Live Messenger and Yahoo Messenger can be used by anyone at no cost. For video conferencing, University of Oulu has fitted several rooms with the necessary equipment. A C K N O W L E D G E M E N T S The study was supported by Campus Futurus as part of the project "Computer assisted leaning and transferable skills in Biochemistry". Antti Isomursu kindly provided web hosting for the prize draw registration system. Lloyd Ruddock, Tuomo Glumoff, Miki Kallio, Emilia Pekkala and Seppo Haapalainen gave helpful comments and suggestions. -- On Tue, Oct 16, 2007 at 12:08 PM, Olli Niemitalo <o(a)iki.fi> wrote: > > Computers and automated methods of data analysis are useful tools. What > are _your_ specific needs as a biochemistry student, teacher, working > biochemist or an employer of biochemists? By answering the following > anonymous survey, you will help guide development of teaching at the > Department of biochemistry, University of Oulu. > > http://www.surveymonkey.com/s.aspx?sm=8ubEm_2fkth4mlQrX_2bUb40YA_3d_3d > > Please answer the survey carefully. It will take about 15 minutes. After > completion, you are entitled to register for a prize draw of two times 150 > euro! Your survey answers will remain anonymous. > > The survey is intended for biochemists only and will stay open until the > end of November. You are welcome to give the link to fellow biochemists > who are not receiving this e-mail. The survey is part of the Campus > Futurus project "Computer assisted learning and transferable skills in > Biochemistry". > > -olli > > _______________________________________________ > Bco mailing list > Bco(a)lists.oulu.fi > http://lists.oulu.fi/mailman/listinfo/bco >

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Kaamos symposium
by Pavlo E. Ardanov 06 Oct '08

06 Oct '08

Dear PhD students, We, the PhD students of the Department of Biology at the University of Oulu, would like to invite you to present your researches in our annual graduate student symposium on 8.-9. December 2008. If your research is related to biology our Kaamos symposium is a good opportunity for you to present and discuss your results in a friendly environment of biology students and senior researches and also exceptional possibility for us to be aware what's going on in related research fields. Presentations should be 15 minutes, plus 5 minutes for questions and discussion. Registration deadline for presentations and posters is the 31st of October. Abstracts should be ready and send to us by the 30th of November. If you want to register for Kaamos symposium or have any questions or suggestions don't hesitate to contact us! Also mail us if you wish to obtain further information about symposium - our web-page is under development at the moment. Hope to see you on our symposium. Best wishes on behalf of this year's committee, Katja Kangas, katja.kangas(a)oulu.fi Julia Schregel, julia.schregel(a)oulu.fi Pavlo Adarnov, pavloard(a)mail.student.oulu.fi Outi Manninen, outi.manninen(a)oulu.fi Marian Sarala, marian.sarala(a)oulu.fi Esa Aalto, esa.aalto(a)oulu.fi

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Seminaari huomenna: Minna Männikkö
by Tuomo Glumoff 06 Oct '08

06 Oct '08

Hei, LuK-kurssin seminaarisarjassa vuorossa huomenna tiistaina 7.10. Dos. Minna Männikkö Biolääketieteen laitokselta. Seminaari alkaa klo 15:00 (tasan) seminaarihuoneessa BK226C. Seminaarin otsikko: Ruston ja luun sairauksien genetiikkaa harvinaisista yleisiin perinnöllisiin sairauksiin. Kiinnostuneet muutkin opiskelijat ja tutkijat tervetuloa! Tuomo ========================================== Tuomo Glumoff, FT Tuomo Glumoff, Ph.D. lehtori, dosentti lecturer and docent Oulun yliopisto University of Oulu Biokemian laitos Dept. Biochemistry PL 3000 BOX 3000 90014 OULUN YLIOPISTO FI-90014 UNIVERSITY OF OULU Finland ========================================== Kontaktitiedot - Contact information: <http://www.biochem.oulu.fi/henkilokunta/glumoff/> www.biochem.oulu.fi/henkilokunta/glumoff/ ========================================== matkapuh. / mobile: +358-(0)50-5226136 ==========================================

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Practical teaching for biochemists
by Lloyd Ruddock 06 Oct '08

06 Oct '08

Dear all, The preliminary timetable for this course is: Week Day Time Hall Teacher Lesson 42 Mon 13.10. 12-15 BK130 Asko Pre teaching 43 Fri 24.10. 14-16 KE1139 Jolene E1b 44 Mon 27.10. 12-15 BK130 Asko Pre teaching 44 Wed 29.10. 10-12 BK226C Lloyd Prep for lab 1 45 Wed 5.11. 8-13 lab Lloyd & co. LabPractical 45 Fri 7.11. 8-13 lab Lloyd & co. LabPractical 46 Tue 11.11. 10-12 L9 Jolene E1b 48 Mon 24.11. 11-13 BK226C Lloyd Prep for lab 2 48 26.-28.11. 8-16 BK226 (comp) Lloyd & co. Lab Practical 49 Wed 3.12. 9-11 BK122 Lloyd Prep for lab 3 49 Wed 3.12. 12-14 BK122 Eva E1a 50 Tue 9.12. 8-16 lab Lloyd & co. LabPractical 50 Wed 10.12. 8-16 lab Lloyd & co. LabPractical Note that each person will supervise one of each biomolecules practicals i.e. one in week 45 (not both); one in week 48 (not all), one in week 50 (not both). The course runs into the Spring term, but this timetable is not yet set. I currently have 8 people signed up on my list: Elina Jokinen Tuija Kallio Marjo Karppinen Essi Karstinen Markus Keskitalo Kati Korhonen Hanna Ojala Susanna Teppo However there have been problems with emails of late, so I might not have everyone on this list who emailed me. Please check and let me know if you are missing. The deadline for signing up is Thursday 9th October. I will assign people into groups on Friday 10th. VBW, Lloyd

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Computer login
by Lloyd Ruddock 06 Oct '08

06 Oct '08

Dear all, In light of the increasing need for MSc level students to access the departmental server directly there has been a change in departmetnal policy. >From now on all MSc level students will be granted a student login to our departmental server for the full 2 years of the MSc. While there are some restrictions on student accounts this level of access for all MSc students is unprecedented, please use these accounts only for study and work related to Biochemistry - if they get abused they will be withdrawn from all students. You will be asked to sign to say that you know that you should not download any material not related to study and work related to biochemistry and that you will not install software. Please respect these simple rules. Logins can be obtained directly from Ari-Pekka. BSc level students remain as before i.e. ad hoc logins given out for specific courses. Best wishes, Lloyd

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