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.
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On Tue, Oct 16, 2007 at 12:08 PM, Olli Niemitalo o@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
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