From owner-chemistry@ccl.net Sat Aug 29 00:21:00 2009 From: "Mihaly Mezei Mihaly.Mezei|mssm.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40111-090829001015-4110-Z14ZLPry3+EE7fzEMGp6rw=-=server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: quoted-printable Content-type: text/plain; charset=windows-1252 Date: Sat, 29 Aug 2009 00:10:02 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei^_^mssm.edu] =3E The stuff above is well written=2C sounds pathetic but it simply doe= s =3E not work in the nowadays world=2E Sorry=2C if this sounds mocking bu= t I =3E recollect a conversation with one smart young guy who complained =3E that girls don=27t pay attention to clever guys like him but always= =3E go for these stupid bullies with muscles=2E I advised him to groom =3E himself=2C use deodorant and clean his teeth=2E He first was offende= d =3E but shortly after thanked me for an advice and in a short while I =3E saw him with one of these =22dream girls=22=2E She happened to be =22= smart=22 =3E too and being not ashamed of his new boyfriend to show up with on =3E the parties her science grades sky rocketed soon =3A) Your story just illustrated the fact that you don=27t need any gimmick t= o get someone interested in science=2C just paying attention to basic pe= rsonal hygiene will do =2E=2E=2E =3E Yes=2C kids go to the rock concerts and sport arenas=2E This attract= s =3E them to music and sport=2E Soon after they start it=2C they find it = all =3E about sweat=2C hard work and tough competition=2C but they are alrea= dy =3E in love=2E=2E=2E So let it be for science as well=2E If we are smart= let us =3E not be whining and hiding in closet but compete with entertainers=2E= =3E After all they also use the best technology available for their own =3E benefit=2E Why not reverse it and use their tricks to get the young =3E souls back to thinking and science=2E One warning ahead=2C don=27t f= orget =3E the purpose of what you do=2C entertainment is an equal drug for =3E those who watch and those who make it=2E It is like a headache or =3E sleeping pill=2E If you take it knowledgeably for purpose=2C it help= s =3E but it does not eliminate the cause of illness but can make you =3E addicted to the pill=2E=2E=2E = =3E =3E Cheers=2C =3E Anatoli Korkin =3E korkin-at-nanoandgiga=2Ecom Well=2C to my =91pathethic=92 mind=2C your suggestion sounds more like g= athering members for a cult than for encouraging students to be a scient= ist=2E I think the quote from the Hungarian playwright Ferenc Molnar is = very relevant here=3A =93Don=92t touch shit=2E Not even with gloves on=2E= Instead of the shit getting glovvy=2C you will end up with the glove ge= tting shitty=94=2E Mihaly Mezei Department of Structural and Chemical Biology=2C Mount Sinai School of M= edicine=2C NYU Voice=3A (212) 659-5475 Fax=3A (212) 849-2456 WWW (MSSM home)=3A http=3A//www=2Emountsinai=2Eorg/Find=2520A=2520Facult= y/profile=2Edo=3Fid=3D0000072500001497192632 WWW (Lab home - software=2C publications)=3A http=3A//inka=2Emssm=2Eedu/= =7Emezei WWW (Department)=3A http=3A//atlas=2Ephysbio=2Emssm=2Eedu From owner-chemistry@ccl.net Sat Aug 29 09:18:01 2009 From: "Alex Henderson alex.henderson{}manchester.ac.uk" To: CCL Subject: CCL: Graph traversal Message-Id: <-40112-090829085116-6096-4NIAWCQ6W/yXP7r60IP90w.:.server.ccl.net> X-Original-From: Alex Henderson Content-Type: multipart/alternative; boundary="------------070107000909030204020905" Date: Sat, 29 Aug 2009 13:12:59 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Henderson [alex.henderson^^manchester.ac.uk] This is a multi-part message in MIME format. --------------070107000909030204020905 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, I'm looking for software (or a library) that will allow me to visualise a directed graph. I need some zoom in/out functionality since my graph contains thousands of nodes. Open source/cross-platform preferred. (Also free of course! :-) Anyone know where I should look? Thanks, Alex --------------070107000909030204020905 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

I'm looking for software (or a library) that will allow me to visualise a directed graph. I need some zoom in/out functionality since my graph contains thousands of nodes.

Open source/cross-platform preferred. (Also free of course! :-)

Anyone know where I should look?

Thanks,
Alex

 

--------------070107000909030204020905-- From owner-chemistry@ccl.net Sat Aug 29 10:28:00 2009 From: "Chris Swain swain*|*mac.com" To: CCL Subject: CCL: Graph traversal Message-Id: <-40113-090829102655-6660-q+XsCNBNVF1FpHkD1ICebA_._server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_UtSV+4G084qX+bc8b5g9HQ)" Date: Sat, 29 Aug 2009 15:26:37 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain.],[.mac.com] --Boundary_(ID_UtSV+4G084qX+bc8b5g9HQ) Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-transfer-encoding: 7BIT Hi, I keep a list of such tools for Mac but many are cross platform. http://homepage.mac.com/swain/Macinchem/Static/data_anal_tools.html Chris On 29 Aug 2009, at 13:12, Alex Henderson alex.henderson{}manchester.ac.uk wrote: > Hi, > > I'm looking for software (or a library) that will allow me to > visualise a directed graph. I need some zoom in/out functionality > since my graph contains thousands of nodes. > > Open source/cross-platform preferred. (Also free of course! :-) > > Anyone know where I should look? > > Thanks, > Alex > > --Boundary_(ID_UtSV+4G084qX+bc8b5g9HQ) Content-type: text/html; charset=US-ASCII Content-transfer-encoding: quoted-printable Hi,

I keep a = list of such tools for Mac but many are cross = platform.


Chris

On 29 Aug 2009, = at 13:12, Alex Henderson alex.henderson{}manchester.ac.uk = wrote:

Hi,

I'm looking for software (or a library) = that will allow me to visualise a directed graph. I need some zoom = in/out functionality since my graph contains thousands of nodes.
=
Open source/cross-platform preferred. (Also free of course! :-)
=
Anyone know where I should look?

Thanks,
= Alex

 

=

= --Boundary_(ID_UtSV+4G084qX+bc8b5g9HQ)-- From owner-chemistry@ccl.net Sat Aug 29 11:45:00 2009 From: "Rajarshi Guha rajarshi.guha ~ gmail.com" To: CCL Subject: CCL: Graph traversal Message-Id: <-40114-090829113642-7136-joc6O4FfksehdL8CWzcl7w^-^server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=0016363b925ef3bf71047248dae1 Date: Sat, 29 Aug 2009 10:45:43 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha],[gmail.com] --0016363b925ef3bf71047248dae1 Content-Type: text/plain; charset=ISO-8859-1 On Sat, Aug 29, 2009 at 8:12 AM, Alex Henderson alex.henderson{} manchester.ac.uk wrote: > Hi, > > I'm looking for software (or a library) that will allow me to visualise a > directed graph. I need some zoom in/out functionality since my graph > contains thousands of nodes. > > Open source/cross-platform preferred. (Also free of course! :-) > Cytoscape LaNet-VI, Pajek (as applications) igraph, Jung, Prefuse (as libraries) -- Rajarshi Guha NIH Chemical Genomics Center --0016363b925ef3bf71047248dae1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Sat, Aug 29, 2009 at 8:12 AM, Alex He= nderson alex.henderson{}manchester.ac.u= k <owne= r-chemistry..ccl.net> wrote:
Hi,

I'm looking for software (or a library) that will allow me to visualise a directed graph. I need some zoom in/out functionality since my graph contains thousands of nodes.

Open source/cross-platform preferred. (Also free of course! :-)

Cytoscape LaNet-VI, Pajek (as applications)
igrap= h, Jung, Prefuse (as libraries)


-- Rajarshi Guha
NIH Chemical Genomics Center
--0016363b925ef3bf71047248dae1-- From owner-chemistry@ccl.net Sat Aug 29 12:27:00 2009 From: "Anatoli Korkin a_korkin%yahoo.com" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40115-090829122526-31232-hfBV1KiH3E5K9OynkLbKbg|server.ccl.net> X-Original-From: Anatoli Korkin Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Sat, 29 Aug 2009 09:25:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [a_korkin,+,yahoo.com] > Your story just illustrated the fact that you don't need=0A> any gimmick = to get someone interested in science, just=0A> paying attention to basic pe= rsonal hygiene will do ...=0A>=0A=0AExactly! Thank you for the point. If sc= ientists would not isolate themselves from the society and eliminate an ima= ge of a "weird geek", their science would be easier accepted by the society= . Why entertainers, doctors and lawyers get higher rewarded by the society?= Do they contribute more to it? I don't think even people from these groups= would say so. One point is clear - those above are more closely connected = to immediate basic needs (I was close even to say "basic instincts") of the= human society, while scientists are more distant by the nature of their pr= ofession. So are "pure artists" who often die starving while generations af= ter them sell their work for a fortune. While the nature of science can not= (and should not!) be changed, a closer ties between scientists and society= via popular education is important. Computational chemistry in fact is ver= y close to this point with its fascinating and artistic images generated by= molecular design software and other jewels of virtual reality. =0A=0A> Well, to my =E2=80=98path= ethic=E2=80=99 mind, your suggestion sounds=0A> more like gathering members= for a cult than for encouraging=0A> students to be a scientist. I think th= e quote from the=0A> Hungarian playwright Ferenc Molnar is very relevant he= re:=0A> =E2=80=9CDon=E2=80=99t touch shit. Not even with gloves on. Instead= of=0A> the shit getting glovvy, you will end up with the glove=0A> getting= shitty=E2=80=9D.=0A>=0A=0AAs far as the "cult gathering", I suggest just o= pposite - making scientists closer to society without being "drugged" by po= wer of politics and entertainment but use them for good will (safe path to = the evil? :) As far as shitty-glovvy alternative, what would you say to the= doctor working on your hemorrhoid problem?=0A=0ACheers,=0AAnatoli Korkin= =0Ahttp://www.nanoandgiga.com/~korkin/=0A=0A=0A =0A> Mihaly Mezei=0A> =0A> = Department of Structural and Chemical Biology, Mount Sinai=0A> School of Me= dicine, NYU=0A> Voice:=C2=A0 (212) 659-5475=C2=A0=C2=A0=C2=A0Fax: (212)=0A>= 849-2456=0A> WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty= /profile.do?id=3D0000072500001497192632=0A> WWW (Lab home - software, publi= cations): http://inka.mssm.edu/~mezei=0A> WWW (Department): http://atlas.ph= ysbio.mssm.edu=0A> =0A> =0A> =0A> -=3D This is automatically added to each = message by the=0A> mailing script =3D-=0A> To recover the email address of = the author of the message,=0A> please change=0A> the strange characters on = the top line to the [a] sign. You=0A> can also=0A> look up the X-Original-Fro= m: line in the mail header.=0A> =0A> E-mail to subscribers: CHEMISTRY[a]ccl.n= et=0A> or use:=0A> =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send= _ccl_message=0A> =0A> E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net= =0A> or use=0A> =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_cc= l_message=0A> =0A> Subscribe/Unsubscribe:=0A> =C2=A0 =C2=A0 =C2=A0 http://w= ww.ccl.net/chemistry/sub_unsub.shtml=0A> =0A> Before posting, check wait ti= me at: http://www.ccl.net=0A> =0A> Job: http://www.ccl.net/jobs=0A> Confere= nces: http://server.ccl.net/chemistry/announcements/conferences/=0A> =0A> S= earch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A> =0A>==0A> =C2=A0 =C2=A0 = =C2=A0=0A> =0A> RTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/=0A> =0A> =0A> =0A=0A=0A From owner-chemistry@ccl.net Sat Aug 29 18:01:00 2009 From: "Basma Ghazal basmaghazal{=}ymail.com" To: CCL Subject: CCL: request Message-Id: <-40116-090829174428-17239-CmF2jIwuX2bb64/HLKUT0Q__server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-607188854-1251582256=:15336" Date: Sat, 29 Aug 2009 14:44:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal###ymail.com] --0-607188854-1251582256=:15336 Content-Type: text/plain; charset=us-ascii Dear All: I need to know why we remove the water? and Why we remove the polar hydrogen? Did we have to add hydoger after that? Thanks --0-607188854-1251582256=:15336 Content-Type: text/html; charset=us-ascii
Dear All:
I need to know why we remove the water?
and Why we remove the polar hydrogen?
Did we have to add hydoger after that?
Thanks

--0-607188854-1251582256=:15336-- From owner-chemistry@ccl.net Sat Aug 29 19:09:01 2009 From: "Kalju Kahn kalju^chem.ucsb.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40117-090829190532-15645-iA0gUcbe9Ggzkc2J7w6ojg*server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 29 Aug 2009 16:05:11 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju-#-chem.ucsb.edu] Good point, Anatoli > Sent to CCL by: Anatoli Korkin [a_korkin,+,yahoo.com] > While the nature of science can not (and > should not!) be changed, a closer ties between scientists and society via > popular education is important. Computational chemistry in fact is very > close to this point with its fascinating and artistic images generated by > molecular design software and other jewels of virtual reality. Another interesting thing going for computational chemistry in this regard is that its tools are easily accessible to general public, compared to the rest of modern chemistry and physics. Kids know computers, kids know how to download stuff (programs and basis sets, including), and they can figure out how to run these programs because of manuals or tips on the web if they want to. Maybe some "academic software" developers could state clearly that everyone is welcome to download it for free for general home/educational use. No, they may not exactly grasp what it means that their calculation is not size consistent or suffers from a severe spin contamination, but they are able to get "results" and make pretty MO pictures, and show vibrating molecules off to their friends. This provides the sense of instant satisfaction, like beating a level in a video game. It releases the packet of dopamine that our brain needs to go on. Cool! Low cost! Safe! Mom and dad would feel well about buying a pair of GTX295 for a birthday to help with offspring's science projects. And who would not like to brag about their kick-ass home supercomputer! Consider any other branch of chemistry for comparison. Well it is mainly experimental. Purifying DNA from bananas, or adding different toothpastes to a Petri dish with colonies of own's microflora is sure a cool thing for seventh or eight grade science projects. But say, you really want to do something that resembles a modern science. Nope, this microwave oven will not work as a PCR thermocycler, and the colorimeter in high-school chem lab probaly will not go down to 260-280 nm. There were times when mixing chemicals that I cannot name under US Patriot Act provided plenty of entertainment but this sort of chemistry does not fly well in modern times. The bottom line is that there is little that a high-school students can do in terms of experimental chemistry at home or school that would be considered cool and exiting by friends and parents, and would provide a quick sense of accomplishment. Coming back to where it all started, I see nothing wrong with using oversimplified models with general audience in mind. Ideally, one would have some links nearby pointing to more rigorous descriptions, and maybe even links to college course pages where these subjects are developed in detail. I would not complain if a student choose to attend, say Iowa State (or Moscow State, or University of Oslo) because watching a video about people dancing like electrons sparked their curiosity, and lead them to downloading a free program like GAMESS (or Firefly, or Dalton). Best wishes, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106