Thursday, June 17, 2010

clone a VDI Virtual Box image for using elsewhere

How robust is this procedure (found here)?
  1. Shut down the virtual machine you would like to copy
  2. In File > Virtualdiskmanager, select the virtual machine disk image you would like to copy, and press the Release button
  3. In a terminal window, issue following command (see virtualbox user manual):
    vboxmanage clonevdi /directory/image1.vdi /directory/image2.vdi
  4. In File > Virtualdiskmanager, add the new disk image you've created in step 3
  5. In the main virtualbox window, press the New button to create a new virtual machine, and link it to the new disk image you've created.

Wednesday, June 9, 2010

Cartoons in biology?? How about: diagram, figure, illustration or schematic

Molecular biologists often refer to depictions of cellular processes or structure as cartoons.  (here is an example).  I think it is a poor word choice.  Cartoon is generally used to indicate a humorous depiction or an unfinished product (i.e., a sketch on a carton), so it is somewhat insulting to the creator of the illustration (unless it is, in fact, unfinished or humorous).  What I think they are trying to say by calling their diagram a cartoon is something like: "do not forget that this diagram is a vast oversimplification of reality!  Proteins are not really boxes and lines are really not protein associations!  Proteins aren't made of ribbons!"  At times, one also gets the feeling they are trying to convey something more, "Our field is so complex, our diagrams are ludicrously simple compared to reality!" or even, "Aren't I cute for calling this a cartoon even though this is a science talk!"

Fortunately, there are several other words suggesting that a depiction is not a precise representation of reality but rather a simplification that serves to emphasize certain facts or relationships, and they don't carry any of cartoon's demeaning connotations: diagram, figure, illustration, schematic.  IMHO, these are vastly preferable for referring to depictions of biological phenomenon.  This seems to be well supported by definitions, synonyms, and word associations:

Merriam-Webster (online)

Etymology: Greek diagramma, from diagraphein to mark out by lines, from dia- + graphein to write — more at carve
Date: 1619
1 : a graphic design that explains rather than represents; especially : a drawing that shows arrangement and relations (as of parts)
2 : a line drawing made for mathematical or scientific purposes

Inflected Form(s): plural sche·ma·ta \-mə-tə\ also schemas
Etymology: Greek schēmat-, schēma
Date: circa 1890
1 : a diagrammatic presentation; broadly : a structured framework or plan : outline
Etymology: Middle English, from Anglo-French, from Latin figura, from fingere
Date: 13th century
2 a : a geometric form (as a line, triangle, or sphere) especially when considered as a set of geometric elements (as points) in space of a given number of dimensions b : bodily shape or form especially of a person c : an object noticeable only as a shape or form
s moving in the dusk>

3 a : the graphic representation of a form especially of a person or geometric entity b : a diagram or pictorial illustration of textual matter


Date: 14th century
2 : something that serves to illustrate: as a : an example or instance that helps make something clear b : a picture or diagram that helps make something clear or attractive

Etymology: Italian cartone pasteboard, cartoon, augmentative of carta leaf of paper — more at card
Date: 1671
1 : a preparatory design, drawing, or painting (as for a fresco)
2 a : a drawing intended as satire, caricature, or humor b : comic strip
3 : animated cartoon
4 : a ludicrously simplistic, unrealistic, or one-dimensional portrayal or version ;


Part  of  Speech:      noun
Definition:     drawing, sketch of form or plan
Synonyms:     big picture, blueprint, chart, description, design, draft, figure, floor plan, game, game plan, ground plan, layout, outline, perspective, representation, rough draft

Part  of  Speech:      noun
Definition:     design
Synonyms:     architecture, arrangement, blueprint, chart, comp, composition, conception, constitution, construction, delineation, depiction, diagram, doodle, drawing, dummy, form, formation, game plan, idea, layout, makeup, map, method, model, outline, paste-up, pattern, perspective, picture, plan, project, scheme, strategy, study, tracery, tracing, treatment

Part  of  Speech:      noun
Definition:     object with design; depiction
Synonyms:     cast, composition, decoration, device, diagram, drawing, effigy, embellishment, emblem, illustration, image, model, mold, motif, motive, ornamentation, pattern, piece, portrait, representation, sketch, statue

Part  of  Speech:      noun
Definition:     drawing, artwork that assists explanation
Synonyms:     adornment, cartoon, decoration, depiction, design, engraving, etching, figure, frontispiece, halftone, image, line drawing, painting, photo, photograph, picture, plate, sketch, snapshot, tailpiece, vignette

Part  of  Speech:      noun
Definition:     funny drawing, often with dialogue or caption
Synonyms:     animation, caricature, comic strip, drawing, lampoon, parody, representation, satire, sketch, takeoff

associated to diagram
1.    chart    weak
2.    graph    weak
3.    draw    v. weak
4.    plan    v. weak
5.    block    v. weak
associated from diagram
1.    chart    medium
2.    picture    medium
3.    diaphragm    weak
4.    drawing    v. weak
5.    graph    v. weak

associated to schema
1.    scheme    strong
2.    axiom    weak
3.    concept    weak
4.    fema    weak
5.    pooh    weak
associated from schema
1.    scheme    strong
2.    database    weak
3.    diagram    weak
4.    paradigm    weak
5.    seem    weak

associated to figure
1.    stick    medium
2.    action    weak
3.    father    weak
4.    shape    weak
5.    authority    v. weak
associated from figure
1.    shape    medium
2.    eight    medium
3.    skate    weak
4.    skating    v. weak
5.    out    v. weak

associated to schematic
1.    plan    strong
2.    scheme    medium
3.    architecture    weak
4.    blueprint    weak
5.    diagram    weak
associated from schematic
1.    blueprint    strong
2.    system    strong
3.    design    medium
4.    drawing    medium
5.    love    medium

associated to illustration
1.    example    medium
2.    drawing    medium
3.    graphic    weak
4.    book    v. weak
5.    capella    v. weak
associated from illustration
1.    picture    strong
2.    drawing    medium
3.    book    weak
4.    cartoon    weak
5.    draw    weak

associated to cartoon
1.    animation    v. weak
2.    simpsons    v. weak
3.    anime    v. weak
4.    disney    v. weak
5.    character    v. weak
associated from cartoon
1.    character    medium
2.    network    weak
3.    animation    weak
4.    comic    v. weak
5.    tv    v. weak