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Uitbreiding van Videoconferencing faciliteiten op HAN campus

12 juni 2014 door Ton Ammerlaan

Er is steeds meer vraag naar Weblectures van docenten die hun verhaal integraal of in korte vorm op video vastleggen ter ondersteuning van hun onderwijs of bij de intake van internationale studenten. In elke faculteit zijn wel camera’s te vinden en worden pakketten als Microsoft Lync, Google Hangout of Skype gebruikt, en diverse service units hebben hun oplossing. Op de HAN campussen zijn 3 webconferencing en videoconferencing faciliteiten beschikbaar: de R31 Arnhem studio die gekoppeld is aan de FEM tegenpool op Laan van Scheut 10, de kleinere studio op Laan van Scheut 2 waar vooral overleg met buitenlandse partners, alumni en afstuderende studenten plaatsvindt, en sinds kort de splinternieuwe GGM studio op K33 D 1.18.

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Useful tools for research in microbiology

23 mei 2014 door Ton Ammerlaan

In order to update the software I am looking into tools that we could use at HAN as well, in addition to CLCBio. Nowadays, molecular biology tools are much more accessible. Here are some online sites for molecular biology I have been recommended:


1. BLAST (NCBI): The Basic Local Alignment Search Tool (BLAST) is an algorithm for comparing primary sequence information. A BLAST search allows you to compare a sequence of interest with a database of sequences for homology. It can be used to align different types of sequences such as amino acids or nucleotides.


2. Ensembl: The Ensembl concept lies in the ability to automatically generate graphical views of gene alignment (and other data) against a reference genome. The nice thing about Ensembl is that you can turn on and off certain features or ‘tracks’ depending on what you want to see. It is also really useful in obtaining some basic information, like transcript length, coding exon number and even GO details.


3. Primer 3: This is a great online tool to help you pick primers. It takes in to account your desired Tm, product size and many more variables. Find it here: http://biotools.umassmed.edu/bioapps/primer3_www.cgi.


4. GEO (NCBI): The Gene Expression Omnibus (GEO) is yet another of the array of tools that NCBI offers. It is basically a public functional genomics repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomics data submitted by the research community. Some journals are now beginning to request that your microarray data be available on this site before publication. This is a really great tool to see how gene expression changes under many different conditions and in many different species.


5. UniProt: This is a high quality and freely accessible database of protein sequence and functional information. Many of the entries are derived from genome sequencing projects and it contains a large amount of information about the biological function of proteins derived from research literature. See: http://www.uniprot.org/.


6. Ingenuity Pathway Analysis (IPA): One of the great things about IPA is that it can be used with or without data. It can help in the analysis of data from expression and SNP microarrays, proteomics and any experiment that generates a gene list, in order to get an insight into molecular interactions, phenotypes and disease processes. IPA also allows you to search for specific information on genes, proteins drugs etc. that can be used to build models or design experiments. Although it is not free, it can be used for a free trial period. Find it here: http://www.ingenuity.com/products/ipa.


7. Reactome: This is a manually curated, peer-reviewed database of biomolecular pathways. It can be used for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis and systems biology.


8. GeneMANIA: Apart from the fun name, this site is quite useful. It finds genes that are related to a single or group of input genes using a large set of functional association data. This includes protein/gene interactions, co-expression and co-localization data. Find it here: http://www.genemania.org.


9. Restriction Mapper:This tool maps sites for restriction enzymes, like endonucleases, in DNA sequences. It even does a ‘virtual digestion’.


10. Molecular Biology Protocols Online: Although this is not really a program or tool, it can be really useful if you need some protocol hints. It has everything from RNA extraction to transfection to cloning. Find it here: http://www.protocol-online.org/prot/Molecular_Biology/.


11 Genecards http://www.genecards.org/ which allows you to instantly get an outline of the known functions, features, domains, expression patterns, splice variants, etc., of any gene I encounter. Search the name or acronym of any gene/protein and it will bring up a page including information compiled from many sources. One of my favorite features (and one of the simplest) is the list of gene/protein aliases for each entry, which has saved me hours of searching the literature for information about genes using obscure acronym.


12. Genome Browser Another must is the UCSC Genome Browser. Use this intuitive interface to surf the genome looking at graphically displayed data from many sources, including most of the data from ENCODE. Exploring regulation of a new gene? A quick search for the gene, turn on a few fields, and you can see, all at once, which tissues it is expressed in, the chromatin state(marks) at the locus, the transcription factors/enhancers that bind its promoter, and countless other valuable data.


Are these useful and did I miss out on my survey so far?


Opslagmogelijkheden voor onderzoeksdata bij HAN

10 december 2013 door Ton Ammerlaan

Voor echte wetenschap is de controleerbaarheid van gegevens heel belangrijk. Datamanagement in de vorm van digitaal opslaan, bewaren en vindbaar maken van gegevens is daarom een must. Waar kunnen HAN onderzoekers hun data opslaan? Hoe doen ze dat goed in hun datamanagement plan? Welke ondersteuning krijgen ze van informatiecoordinatoren?
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EU lijst van aPlanet van ICT hulpmiddelen in onderwijs

21 juni 2013 door Ton Ammerlaan

aPlanet is an EU project that lists useful tools for classrooms: an overview and resource guide is listed on http://aplanet-project.eu/index.php.

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Videopresentaties maken met present.me

31 mei 2013 door Ton Ammerlaan

Toe aan je klas flippen? Presentaties met videoinstructies voorzien is handig voor kennisclips, online presentaties aan begeleiders of studenten en voor algemene uitleg over een kwestie. Met Present.me kun je Powerpoint, PDF, Excel, Word, Google Docs of Open Office met de klik van een knop uploaden naar Present.me. Ze converteren de bestanden naar een formaat zodat ze klaar staan om je commentaar en toelichting bij op te nemen mbv een webcam. Present.me zet het dan bij elkaar. Een account is gratis (= 60 min, max. 10 opnames per maand) maar je kunt ook uitgebreider werken. HAN gebruikt hiervoor presentations2go en de video.han.nl server.
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